emboss-test 6.6.0+dfsg-6build1 / usr / share / EMBOSS / test / qatest.dat

###########################################################################
# Things to do
#
#
###########################################################################

# This is the qatest.dat file that is used by scripts/qatest.pl
#
# The script should be run from the directory test/qa
#
# Additional input data is expected to be found in the directory test/data
#
# If no argument is given to the script it will run through all of the
# entries in this file. If an argument is supplied it will search for
# the entry whose ID name matches the argument and will run that one.
#
# To run the script and retain the files created during the test, use
# ../../scripts/qatest.pl key:-kk
# 
# The results of the QA tests will be stored in the file
# test/qa/qatest.log
# 
# Typical example entry for an EMBOSS package program (AP line)
# See below for AA/AB (EMBASSY) and AQ (make check) entries
# 
# ID programname-ex (the ID name of this test)
# UC text (not used in the QA test - used in the HTML documentation)
# AP programname (the name of the application to test)
# CL (the command-line arguments to use after the application name)
# IN (a response to a prompt for input using the default)
# IN text (a response to a prompt using a non-default input)
# IK text (input keystrokes, not responses to prompts)
# FI filename (an expected output filename)
# FZ integer (the expected size in bytes of the above filename)
# FC integer (the expected number of lines in the above file)
# FP /regexp/ (an expected perl regular expression in the above file)
# FP integer /regexp/ (a regexp that is expected integer number of times)
# FI stderr (these are standard checks on the expected error reports)
# FC = 2
# FP 0 /Warning: /
# FP 0 /Error: /
# FP 0 /Died: /
# // (marks the end of the entry)
# 
# ID identifier
# 	The identifier is formed from the name of the application being 
#	tested and a tag to indicate what sort of test is being performed. 
#	The identifier is used to create a directory test/qa/<identifier>.
#	Typical tags are:
#	-ex	= example used to create the HTML documentation
#	-ex2, -ex3	= further examples used in the documentation
#               In general, all documentation examples should have tests
#               to check the documentation is correct.
# 	-keep If the test has a "DL keep" line the resulting files are kept.
#             Used for database indexing - later tests will use the results!
#       -fail Testing a failure condition (ER line)
# AA Application name for an EMBASSY package application.
#	This is used for the command line and for reporting statistics.
#       The application must be built by "make" for the EMBASSY package
#       defined in the AB line for this test definition.
#       If the application is not found, qatest can assume this
#       EMBASSY package was not installed.
# AB EMBASSY package name
#       Used to inform the qatest script that a test depends on
#        installation of an EMBASSY package and may fail to find the binary.
# AP Application name for EMBOSS application
#	This is used for the command line and for reporting statistics.
#       The application must be a standard EMBOSS application, built by make.
#       The test must succeed.
# AQ Application name for "make check" application
#	This is used for the command line and for reporting statistics.
#       The application must be built by "make check".
#       The qatest script will look in the build directory as this
#       application will not be installed.
#       If the application is not found, qatest can assume "make
#       check" was not run.
# CC Comment
#	Used in commenting on failed tests
#       This comment will appear in the test output on failure as a guide
#       to an acceptable failure condition (check the error message too!)
#       See ## lines for general comments within the definition
# CL Command line
#	(Optional)
#	This is the rest of the command line.
#       Multiple CL lines are appended with a space in between.
# DI Directory
#       Name of a directory created in the results directory
#       No tests currently for the contents, but a QQ postprocessing
#       command could be used to list the contents to another file.
# DL 'success' or 'all' or 'keep'
#	(Optional)
#	'success' = delete the test directory on success (the default)
# 	'all' = delete the test directory always
#	'keep' = keep the test results directory always
#                (used if another test reuses the results,
#                 e.g. database indexing)
# ER error return code
#	(Optional)
# 	Error code expected.
#       Used for tests that are test failure conditions.
#       The test reports an error if the error code is not found
# FC [<=>] number
#	= nn Number of lines
#       > nn More than nn lines
#       < nn Less than nn lines
# FI File name 
#	(Required for all output files created)
#	stdout and stderr are assumed to exist and be empty unless stated.
# FP File pattern
#	(Required for all non stdout and stderr files)
#	perl /regexp/ to be found in the preceeding 'FI' file.
#	The /regexp/ may be preceded by an optional count to check exact
#	number. 
#       As an extra check, stderr (which often contains the user prompts)
#       should be checked for absence of warning, error and died messages.
# FZ [<=>] number 
#	(Required for all non stdout and stderr files)
#	File size test on the preceeding 'FI' file.
#	The file size may be qualified with an optional relation '=', '>' etc.
#	Implicit test for zero size stdout/stderr unless stated.
# IC text
#	(Optional)
# 	This information is not used in the QA testing.
# 	It is used by scripts/makeexample.pl when creating the HTML
#	documentation files to annotate the input.
# IN Line input
#	(Required for each prompted input)
#	If there is nothing on the line, then an empty line is input to the
#	application. (Obvious really, but needs to be said)
#       Care is needed if standard options are added/removed from the program.
# OC text
#	(Optional)
# 	This information is not used in the QA testing.
# 	It is used by scripts/makeexample.pl when creating the HTML
#	documentation files to annotate the output.
# PP Preprocessor command
#	(Optional)
#       Command executed (by /bin/sh) before the test.
#       Each PP line is a separate command. Long lines are not concatenated.
#	e.g. Set an environment variable required by the application.
#	The variable should always be exported (this is /bin/sh), for example:
#	PP EMBOSS_ACDROOT=../../acd
#	PP export EMBOSS_ACDROOT
# QQ Postprocessor command
#	(Optional)
#       Command executed (by /bin/sh) after the test.
#       Each QQ line is a separate command. Long lines are not concatenated.
#	Not used at present. Most likely application is to list the
#       contents of a directory to another file, which can then be
#       tested for size and patterns.
# RQ required
#       Required external programs. For example, srs for tests that
#       use getz, or clustalw for emma
# TI seconds
#       Timeout for test. The default is 60 seconds. Some examples
#       can take longer on a heavily loaded system.
# UC text
#	(Optional)
# 	This information is not used in the QA testing.
# 	It is used by scripts/makeexample.pl when creating the HTML
#	documentation files to annotate the examples of usage.
# ## Comment 
#	(Optional)
#	This is a comment.
#	Double # is required.
#       This is only a comment in the entry and is not reported
#       (use CC lines for comments that appear on failure)


####################
# Command line tests
####################

ID acdc-0001
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0002
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -aint 5 -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0003
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -ai 5 -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0004
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 -sbegin 5 -send 1000 tembl:x13776 x.x -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//


ID acdc-0005
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 -sbegin 5 -send 1000 x.x -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0006
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest -sbegin 5 -send 1000 tembl:x13776 tembl:x13776 x.x -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0007
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -sbegin 5 -send 1000  -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0008
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x
CL  -sbegin_asequence 5 -send_asequence 1000 -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0009
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -sbegin_as 5 -send_as 1000  -auto
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
//

ID acdc-0010
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest -help
FI stderr
FZ = 1391
FP /^Version: EMBOSS:6\.\d+\.[\d.]+\n/
FP 3 / qualifiers:\n/
FP 4 / qualifiers:/
FP 1 /^ +\[-asequence\] +sequence +Sequence filename and optional format, or\n/
FP 1 /^ +\[-bsequence\] +sequence +Sequence filename and optional format, or\n/
FP 2 /^ +\[-[a-z]sequence\] +sequence +Sequence filename and optional format, or\n/
FP /   [-]testalen           string     asequence length \.\.\./
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acdc-0011
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest -help -verbose
FI stderr
FZ = 4978
FP /^Version: EMBOSS:6\.\d+\.[\d+.]+\n/
FP 31 /   boolean /
FP  9 /   integer /
FP 28 /   string /
FP /   [-]testalen           string     asequence length \.\.\./
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acdc-0012
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -debug
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x.x
FZ = 0
FI x13776.fasta
FZ = 0
FI x13776.out2
FZ = 0
FI qatest.dbg
FP /seqinUsaProcess 'tembl:x13776'/
FP 0 /^Memory usage /
//

ID acdc-ex
AP acdc
CL antigenic
IN tsw:actb1_takru
IN
IN
FI actb1_takru.antigenic
FZ = 0
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acdlog-check
AP acdlog
CL antigenic
IN tsw:actb1_takru
IN
IN
FI actb1_takru.antigenic
FZ = 0
FI antigenic.acdlog
FC = 6200
FP 55 /^acdProcess/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acdpretty-ex
AP acdpretty
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest
FI qatest.acdpretty
FZ = 847
FP 2 /[\#]/
FP 3 /^string:/
FP 12 /^[a-z]+: /
FI stdout
FC = 1
FP /^Created qatest\.acdpretty\n/
//

ID acdrelations-ex
AQ acdrelations
PP mkdir ./acdfiles
PP cp ../../../emboss/acd/antigenic.acd ./acdfiles
QQ rm -rf ./acdfiles
CL -intypefile ../../../emboss/acd/knowntypes.standard
IN
IN acdfiles
IN .
FI stderr
FC = 5
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI antigenic.acd
FC = 50
FP 5 /relations: /
//

ID acdtable-ex
AP acdtable
CL antigenic
FI stderr
FC = 54
FP 9 /[<]tr/
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acdtrace-ex
AP acdtrace
CL antigenic
IN tsw:actb1_takru
IN
IN
FI actb1_takru.antigenic
FZ = 0
FI stderr
FC = 20
FP 9 /^Trace: +\d+/
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acdvalid-ex
AP acdvalid
CL antigenic
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

####################
# ACD parsing errors
####################

ID acd-nofile
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL nofile
FI stderr
FZ > 0
FP /Error: File \.\.[\/\\]\.\.[\/\\]acd[\/\\]nofile\.acd line 0: ACD file not opened\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acd-noappl
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noappl
FI stderr
FZ > 0
FP /Error: File .*noappl\.acd line 4: Application definition required at start\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acd-secondappl
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL secondappl
FI stderr
FZ > 0
FP /Error: File .*secondappl\.acd line 9: Application definition allowed only at start\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acd-noleftq
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noleftq
FI stderr
FZ > 0
FP /Error: File .*noleftq\.acd line 7: \(output\) Failed to find '\[' for section output\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acd-noleftsec
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noleftsec
FI stderr
FZ > 0
FP /Error: File .*noleftsec\.acd line 5: \(output\) Failed to find '\[' for section output\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acd-noleftappl
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noleftappl
FI stderr
FZ > 0
FP /Error: File .*noleftappl\.acd line 3: \(noleftappl\) Failed to find '\[' for application noleftappl\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acd-noendsec
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noendsec
FI stderr
FZ > 0
FP /Error: Section 'output' has no endsection\n/
FP /Error: Section 'input' has no endsection\n/
FP 2 /Error: Section '[a-z]*' has no endsection\n/
FP /Error: File .*noendsec\.acd line 13: Unclosed sections in ACD file\n/
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
//

ID acd-noquote
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noquote
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*noquote\.acd line 5: \(outtest\) Unexpected end of file, no closing quote\n/
//

ID acd-novalue
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL novalue
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*novalue\.acd line 5: \(outtest\) Unexpected end of file, attribute value not found\n/
//

ID acd-badstage
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL badstage
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*badstage\.acd line 5: Unrecognized token 'dingsbum'\n/
//

ID acd-calcparam
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL calcparam
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*calcparam\.acd line 22: [(]outtest[)] 'parameter' attribute cannot use a variable\. It is used .* been set\n/
//

ID acd-noapplname
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noapplname
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*noapplname\.acd line 3: Bad or missing application name '\['\n/
//

ID acd-badapplname
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL badapplname
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*badapplname\.acd line 3: Bad or missing application name 'run[*]123'\n/
//

ID acd-noqualname
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noqualname
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*noqualname\.acd line 5: Bad or missing qualifier alphabetic name '\['\n/
//

ID acd-badqualname
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL badqualname
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*badqualname\.acd line 5: Bad or missing qualifier alphabetic name 'sequence1'\n/
//

ID acd-badalias
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL badalias
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*badalias\.acd line 5: Bad syntax qualifier alias name 'file2'\n/
//

ID acd-nocolon
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL nocolon
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*nocolon\.acd line 5: Expected ':' not found after 'param'\n/
//

ID acd-badendsec
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL badendsec
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*badendsec\.acd line 14: Bad endsection 'fred', current section is 'output'\n/
//

ID acd-endsecextra
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL endsecextra
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*endsecextra\.acd line 18: Bad endsection 'fred', not in a section\n/
//

ID acd-dupname
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL dupname
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*dupname\.acd line 14: \(outtest\) Name 'outtest' not unique at line 16\n/
//

ID acd-dupalias
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL dupalias
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*dupalias\.acd line 14: \(outputfile\) Name\/Alias 'outtest'\/'outputfile' not unique at line 16\n/
//

ID acd-ambigtype
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL ambigtype
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*ambigtype\.acd line 16: ambiguous acd type seqo \(seqout,seqoutall,seqoutset\)\n/
//

ID acd-ambigvar
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL ambigvar tembl:x13776 -auto
FI stderr
FZ > 0
FP 1 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*ambigvar\.acd line 9: Failed to resolve variable 'seq'\n/
FP /Warning: ambiguous item seq \(sequence,seqmod\)\n/
//

ID acd-undefvar
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL undefvar tembl:x13776 -auto
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*undefvar\.acd line 7: Variable 'seqmod' not yet defined\n/
//

ID acd-leftend
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL leftend
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*leftend\.acd line 5: \(outtest\) End of file looking for '\]'\n/
//

ID acd-valend
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL valend
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*valend\.acd\ line 5: \(outtest\) End of file looking for '\]'\n/
//

ID acd-noattname
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL noattname
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*noattname\.acd line 5: \(outtest\) Bad or missing attribute name 'requ1red'\n/
//

ID acd-dupassoc
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL dupassoc
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*dupassoc\.acd line 5: \(sbegin\) Associated qualifier 'sbegin' clashes with 'sbegin' in ACD file\n/
//

ID acd-dupassocb
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL dupassocb
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*dupassocb\.acd line 5: \(mybool\) Associated qualifier 'sbegin' clashes with 'mybool'\/'sbegin' in ACD file\n/
//

ID acd-wrongattr
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL wrongattr
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*wrongattr\.acd line 7: \(outtest\) Attribute 'wanted' unknown\n/
//

ID acd-ambigdefattr
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL ambigdefattr tembl:x13776 -filter
FI stderr
FZ > 0
FP 1 /Warning: Ambiguous name/token 'd' \(debug,die\)/
FP 1 /Error: /
FP 0 /Died: /
FP /Error: File .*ambigdefattr\.acd line 3: \(ambigdefattr\) Attribute or qualifier 'd' ambiguous \(debug,die\)\n/
//

ID acd-ambigassoc
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL ambigassoc
FI stderr
FZ > 0
FP 1 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP /Warning: Ambiguous name/token 'f' \(fformat,fopenfile\)\n/
FP /Error: File .*ambigassoc\.acd line 8: \(asequence\) Attribute or qualifier 'f' ambiguous \(fformat,fopenfile\)\n/
//

ID acd-mixedcase
AP acdpretty
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL mixedcase
FI stderr
FZ > 0
FP 1 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Warning: File .*mixedcase\.acd line 16: Automatically converting 'testA' to lower case\n/
FI mixedcase.acdpretty
FZ > 0
FP /: testa /
FI stdout
FC = 1
FP /Created mixedcase\.acdpretty\n/
//

ID acd-testarray
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testarray
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP 1 /^Error: .*testarray\.acd line 8: \(numlist\) Array attribute size: 0 less than 1/
//

ID acd-attralias
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testalias
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FP 1 /^Error: .*testalias\.acd line 22: \(hstring\) Attribute 'requ' unknown/
//

## Command line validation tests
## Handling of associated qualifiers

ID acdc-badqual
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testassoc tembl:v00294 tembl:x13776 -sbegin_a 10
IN
IN
FI stderr
FZ > 0
FP 1 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Warning: Ambiguous master qualifier 'a' in sbegin_a \(auto,asequence,atest\)/
FP /Died: Unknown qualifier -sbegin_a/
//

ID acdc-ambigqual
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -a 5 -auto
ER 1
FI stderr
FP 1 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Warning: ambiguous qualifier 'a' \(auto,asequence,aint\)/
FP /Died: Unknown qualifier -a\n/
//

ID acdc-missing
AP acdc
## "" as a parameter is a missing value treated as an empty string
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 "" x.x
ER 1
FI stderr
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: Failed to open filename ''\n/
FP /Error: Unable to read sequence ''\n/
FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/
//

ID acdc-missing2
AP acdc
## "" as a qualifier value is a missing value treated as an empty string
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 -bsequence="" x.x
ER 1
FI stderr
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: Failed to open filename ''\n/
FP /Error: Unable to read sequence ''\n/
FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/
//

ID acdc-missing3
AP acdc
## Empty qualifier value is a missing value treated as an empty string
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 -bsequence= x.x
ER 1
FI stderr
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: Failed to open filename ''\n/
FP /Error: Unable to read sequence ''\n/
FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/
//

ID acdc-noprefixvalue
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -auto -nologic=Y
ER 1
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Died: 'no' prefix used with value for '-nologic=Y'\n/
//

ID acdc-noprefixbad
AP acdc
## no nullok attribute for this type
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -auto -nooutdir
ER 1
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Died: 'no' prefix invalid for '-nooutdir'\n/
//

ID acdc-noprefixbad2
AP acdc
## nullok attribute is false
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -auto -notestalen
ER 1
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Died: 'no' prefix invalid for '-notestalen'\n/
//

ID acdc-novalue
AP acdc
## nullok attribute is false
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -auto -testalen
ER 1
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Died: Value required for '-testalen'\n/
//

ID acdc-novalue2
AP acdc
## nullok attribute is false
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatest tembl:x13776 tembl:x13776 x.x -auto -testalen -testblen
ER 1
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Died: Value required for '-testalen' before '-testblen'\n/
//

ID acdc-codebad
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
PP EMBOSS_LANGUAGE=bad
PP export EMBOSS_LANGUAGE
CL qatest -help
ER 1
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 1 /Died: /
FP /Died: Bad format in codes file \.\.[\/\\]\.\.[\/\\]acd[\/\\]codes\.bad after 'defbool "Yes or No"'\n/
//

ID acdc-codemissing
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
PP EMBOSS_LANGUAGE=missing
PP export EMBOSS_LANGUAGE
CL qatest -help
FI stderr
FP 1 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Warning: Code file \.\.[\/\\]\.\.[\/\\]acd[\/\\]codes\.missing not found\n/
//

ID acdc-testassoc
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testassoc tembl:v00294 tembl:x13776
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 1113:/
FP /Bsequence end 2167:/
//

ID acdc-testassoc2
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## -send at the start should work on both sequences
CL testassoc -send -1001 tembl:v00294 tembl:x13776
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 1167:/
//

ID acdc-testassoc3
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## -send after first sequence should work on first sequence
CL testassoc tembl:v00294 -send -1001 tembl:x13776
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 2167:/
//

ID acdc-testassoc4
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## -send after second sequence should work on second sequence
CL testassoc tembl:v00294 tembl:x13776 -send -1001
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 1113:/
FP /Bsequence end 1167:/
//

ID acdc-testassoc5
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## -send after another qualifier should work on all sequences
CL testassoc tembl:v00294 tembl:x13776 -ctest "fred" -send -1001
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 1167:/
//

ID acdc-testassoc6
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## Numbered -send for first sequence
CL testassoc tembl:v00294 tembl:x13776 -ctest "fred" -send1 -1001
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 2167:/
//

ID acdc-testassoc7
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## Numbered -send for first sequence
CL testassoc  -send1 -1001 tembl:v00294 tembl:x13776 -ctest "fred"
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 2167:/
//

ID acdc-testassoc8
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## Numbered -send for first sequence
CL testassoc  tembl:v00294 tembl:x13776 -send1 -1001 -ctest "fred"
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 2167:/
//

ID acdc-testassoc9
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## Numbered -sformat for first sequence makes -send global
CL testassoc  tembl:v00294 tembl:x13776 -sformat1 embl -send -1001 -ctest "fred"
IN
IN
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Asequence end 113:/
FP /Bsequence end 1167:/
//

ID acdc-toomanyparam
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
## Numbered -sformat for first sequence makes -send global
CL testassoc  tembl:v00294 tembl:x13776 tembl:k00650
IN
IN
FI stderr
FZ > 0
FP /^Error: Argument 'tembl:k00650' : Too many parameters 3\/2\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
//

ID acdc-alignbadformat
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testalign -aformat fred
IN
FI stderr
FZ > 0
FP /Error: Unknown alignment format 'fred'\n/
FP /Died: Alignment option -atest: Validation failed\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID acdc-alignbadminseq
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testalign
IN
FI stderr
FZ > 0
FP /Error: Alignment format pair specifies at least 2 sequences, alignment has only 0\n/
FP /Died: Alignment option -atest: Validation failed\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID acdc-alignbadmaxseq
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testalignpair
IN
FI stderr
FZ > 0
FP /Error: Alignment format pair specifies at most 2 sequences, alignment has 3\n/
FP /Died: Alignment option -atest: Validation failed\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID acdc-alignbadwidth
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testalignok -awidth 9
IN
FI stderr
FZ > 0
FP 1 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Warning: Alignment width \(-awidth=9\) too narrow, reset to 10\n/
FI outfile.testalignok
FZ = 0
//

ID acdc-funconeof
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL oneof
IN thr
IN 2
FI stderr
FZ > 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP / Pick a number /
//

ID acdc-funconeoffalse
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL oneof
IN two
FI stderr
FZ > 0
FP 1 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP /Warning: integer value out of range 0 less than \(reset to\) 1\n/
//

ID acdc-nodatafile
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL datafile -pepdatafile badname.dat
IN
FI stderr
FZ > 0
FP /Error: Unable to open data file 'badname\.dat' for input\n/
FP /Died: datafile terminated: Bad value for '-pepdatafile' and no prompt\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID acdc-listambig1
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testlist 
IN f
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: 'f' is ambiguous \(fa,four,fb,five\)\n/
FP /Error: Bad menu option 'f'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-listambig2
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testlist 
IN t
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: 't' is ambiguous \(two,three\)\n/
FP /Error: Bad menu option 't'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-listbad
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testlist 
IN x
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: 'x' is not a valid menu option\n/
FP /Error: Bad menu option 'x'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
FP /Accepted short codes are: a,b,c,fa,fb\n/
//

ID acdc-listmax
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testlist 
IN a,b,c,four
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: Menu allows no more than 3 values\n/
FP /Error: Bad menu option 'a,b,c,four'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-listmin
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testlist 
IN 
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: Menu needs 1 value\n/
FP /Error: Bad menu option ''\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-reportbadformat
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testreport -rformat fred
IN 
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
FP /Error: Unknown report format 'fred'\n/
FP /Died: Report option -rtest: Validation failed\n/
//

ID acdc-reportbadtaglist
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testreporttags
IN 
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 0 /Died: /
FP /Error: Bad report taglist at ' str s=String'\n/
FP /Error: File .*testreporttags\.acd line 8: \(rtest\) Bad tag list for report\n/
//

ID acdc-selectambig
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testselect
IN f
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: 'f' is ambiguous \(four,five\)\n/
FP /Error: Bad select option 'f'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-selectbad
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testselect
IN x
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: 'x' is not a valid selection list option\n/
FP /Error: Bad select option 'x'\n/
FP /Accepted values are: one,two,three,four,five\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-selectmax
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testselect
IN one,two,thr,four
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: Selection list allows no more than 3 values\n/
FP /Error: Bad select option 'one,two,thr,four'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-selectmax2
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testselect 
IN 1,2,3,4
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: Selection list allows no more than 3 values\n/
FP /Error: Bad select option '1,2,3,4'\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-selectmin
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL testselect
IN 
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FP /Error: Selection list needs 1 value\n/
FP /Error: Bad select option ''\n/
FP /Error: Unable to get reply from user - end of standard input\n/
//

ID acdc-retry
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
PP EMBOSS_ACDPROMPTS=2
PP export EMBOSS_ACDPROMPTS
CL testselect
IN 6
IN 7
FI stderr
FZ > 0
FP 0 /Warning: /
FP 4 /Error: /
FP 1 /Died: /
FP 2 /Error: Bad select option '[1-9]'\n/
FP /Died: testselect terminated: Bad value for '-stest' and no more retries\n/
//

ID acdc-badadvanced
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
PP EMBOSS_ACDPROMPTS=2
PP export EMBOSS_ACDPROMPTS
CL testselect -numtest fred
IN 5
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
FP /Error: Invalid integer value 'fred'\n/
FP /Died: testselect terminated: Bad value for '-numtest' and no prompt\n/
//

ID acdc-badauto
AP acdc
ER 1
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
PP EMBOSS_ACDPROMPTS=2
PP export EMBOSS_ACDPROMPTS
CL testselect -stest 6 -auto
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP 1 /Error: Bad select option '[1-9]'\n/
FP /Died: testselect terminated: Bad value for '-stest' with -auto defined\n/
//

##########################
# .embossrc parsing errors
##########################

ID nam-badsummary
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/badsummary.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 1 /Died: /
FP /Error: File .*\.embossrc line 2: Error\(s\) found in included file [$]emboss_badfile \(\.\.[\/\\]\.\.[\/\\]rc[\/\\]badsummary.rc\)\n/
FP /Died: Error\(s\) in configuration files\n/
//

ID nam-badtype
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/badtype.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 3 /Error: /
FP 1 /Died: /
FP /Error: File .*badtype\.rc line 1: Invalid definition type 'this'\n/
FP /Error: File .*badtype\.rc line 1: Invalid definition type 'badtype'\n/
FP /Error: File .*\.embossrc line 2: Error\(s\) found in included file [$]emboss_badfile \(\.\.[\/\\]\.\.[\/\\]rc[\/\\]badtype.rc\)\n/
//

ID nam-badset
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/badset.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: File .*badset\.rc line 7: Unexpected end of file in SET definition\n/
//

ID nam-baddb
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/baddb.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: File .*baddb\.rc line 3: Unexpected end of file in DBNAME definition\n/
//

ID nam-badresattr
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/badresattr.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: File .*badresattr\.rc line 3: Bad attribute 'badattr' for resource 'badresource'\n/
//

ID nam-badinclude
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/badinclude.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
FP /Error: File .*\.embossrc line 2: Failed to open include file '[$]emboss_badfile'/
//

ID nam-includeagain
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/includeagain.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: File .*includeagain\.rc line 3: [$]emboss_badfile \(\S+\) already read \.\.\. skipping\n/
//

ID nam-dbempty
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/dbempty.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 5 /Error: /
FP 1 /Died: /
FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no attributes\n/
FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no format definition\n/
FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no type definition\n/
FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no access method definition\n/
//

ID nam-dbunknowns
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/dbunknowns.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 4 /Error: /
FP 1 /Died: /
FP /Error: File .*dbunknowns\.rc line 4: Database 'unknowns' format: 'noformat' unknown for type 'nosuchtype'\n/
FP /Error: File .*dbunknowns\.rc line 4: Database 'unknowns' method: 'notknown' unknown for type 'nosuchtype'\n/
FP /Error: File .*dbunknowns\.rc line 4: Database 'unknowns' type: 'nosuchtype' unknown\n/
//

ID nam-rsempty
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/rsempty.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /Error: File .*rsempty\.rc line 3: Resource 'empty' has no attributes\n/
//

ID nam-dbnoquote
AP showdb
ER 1
PP EMBOSSRC=../../rc
PP export EMBOSSRC
PP EMBOSS_BADFILE=../../rc/dbnoquote.rc
PP export EMBOSS_BADFILE
FI stderr
FZ > 0
FP 0 /Warning: /
FP 4 /Error: /
FP 1 /Died: /
FP /Error: File .*dbnoquote\.rc line 4: '\]' found, unclosed quotes in 'unclosed single quotes'\n/
FP /Error: File .*dbnoquote\.rc line 8: '\]' found, unclosed quotes in 'unclosed double quotes'\n/
FP /Error: File .*dbnoquote\.rc line 12: '\]' found, unclosed quotes in 'unclosed mixed quotes''\n/
//

#######################
# Associated qualifiers
#######################


ID qual-ufo
AP seqret
CL ../../data/hba.fa -feat -ufo ../../data/hba.gff
CL -auto -sf fasta
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 0
FI hba_human.fasta
FC = 4
FP /^>HBA_HUMAN /
FI hba_human.gff
FC = 161
FP /^##gff-version 3\n/
FP /^#!Type Protein\n/
FP /^##sequence-region HBA_HUMAN 1 141\n/
//

ID qual-ufo-noid
AP seqret
CL ../../data/noid.fa -feat -ufo ../../data/noid.gff -sid HBA_HUMAN -sprot
CL -stdout -auto -sf fasta
FI stderr
## GFF output truncated to match the length of the input sequence
## Type DNA because the input sequence is.
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 2
FP /^>HBA_HUMAN/
FI stdout.gff
FC = 28
FP /^##gff-version 3\n/
FP /^#!Type Protein\n/
FP /^##sequence-region HBA_HUMAN 1 19\n/
FP 2 /^HBA_HUMAN\tSWISSPROT\tnatural_variant_site\t19\t19\t/
FP 0 /^HBA_HUMAN\tSWISSPROT\tnatural_variant_site\t20\t20\t/
FP  /\tID=HBA_HUMAN.4;note=ACETYLATION;comment=IN VARIANT THION/
FP  /THIONVILLE%3B WHERE THE INITIATOR MET IS NOT CLEAVED\n/
//

ID qual-sid
AP seqret
CL ../../data/noid.fa
CL -stdout -auto -sf fasta -sid fred
## Fails to use -sid in the output
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 2
FP /^>fred/
//

ID qual-sid2
AP seqret
CL ../../data/noid.fa
CL -stdout -auto -sf fasta -sid fred -osf ncbi
## Fails to use -sid in the output
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 2
FP /^>gnl\|unk\|fred/
//

ID qual-sdb
AP seqret
CL ../../data/hba.fa
CL -stdout -auto -sf fasta -sdb fred
## noid.fa has no sequence ID
## This upsets the feature reading
## Error GFF Group field for table ''
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 4
FP /^>HBA_HUMAN/
//

ID qual-sdb2
AP seqret
CL ../../data/hba.fa
CL -stdout -auto -sf fasta -sdb fred -osf ncbi
## noid.fa has no sequence ID
## This upsets the feature reading
## Error GFF Group field for table ''
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 4
FP /^>gnl[|]fred[|]HBA_HUMAN /
//

ID qual-osdb
AP seqret
CL ../../data/hba.fa
CL -stdout -auto -sf fasta -osdb fred
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 4
FP /^>fred:HBA_HUMAN /
//

ID qual-osdb2
AP seqret
CL ../../data/hba.fa
CL -stdout -auto -sf fasta -osdb fred -osf ncbi
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 4
FP /^>gnl[|]fred[|]HBA_HUMAN /
//

ID qual-osdb3
AP seqret
CL ../../data/hba.fa
CL -stdout -auto -sf fasta -sdb jim -osdb fred -osf ncbi
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 4
FP /^>gnl[|]fred[|]HBA_HUMAN /
//

###############################################################
#
# DAS sequence/feature access methods
#
###############################################################

ID cachedas-ex
TI 600
AP cachedas
CL -servername tdas -auto
CL -cachefile ~/.embossdata/qatests.server.dasregistry
QQ cp ~/.embossdata/qatests.server.dasregistry .
FI qatests.server.dasregistry
FP 1 /^DBNAME uniprot /
FI stdout
FC > 30
FP /embl/
//

ID cachedas-ensembl
AP cachedas
TI 300
CL -servername tensembldasserver -auto
CL -cachefile ~/.embossdata/qatests.server.ensembldasserver
QQ cp ~/.embossdata/qatests.server.ensembldasserver .
FI qatests.server.ensembldasserver
FP /^DBNAME Ailuropoda_melanoleuca/
FI stdout
FC > 30
FP /embl/
//

ID dasregistry-noseqsupport
AP seqret
CL tdas:BacAbs:Q7DDU3 -sbegin 1 -send 10 stdout -auto
ER 1
FI stderr
FC > 2
FP 1 /no match to query type 'sequence'/
FP 1 /Died: /
//

ID dasregistry-featquery-range
AP featcopy
CL tensembldasserver:Homo_sapiens_GRCh37_transcript:10[32889611:32973347] stdout -auto
FI stdout
FP 2 /Target=ENST00000375030/
FP 2 /Target=ENST00000375028/
//

ID dasregistry-featquery-type
AP featcopy
CL "tensembldasserver:Homo_sapiens_GRCh37_reference-{segment:11 & type:supercontig}" stdout -auto
FI stdout
FP 4 /supercontig/
//

ID dasregistry-uniprot
AP seqret
CL tdas:uniprot:P00280 -sbegin 1 -send 10 stdout -auto
FI stdout
FC = 2
FP 1 /^>P00280/
FP 1 /MLAKATLAIV/
//

ID dasregistry-uniprot-multipleseqs
AP seqret
CL "tdas:uniprot:{P00280, p12344}" stdout -auto
FI stdout
FC = 13
FP 1 /^>P00280/
FP 1 /MLAKATLAIV/
FP 1 /^>P12344/
FP 1 /MALLHSGRFL/
//

ID dasregistry-uniparc
AP seqret
CL tdas:uniparc:UPI000000000A -sbegin 1 -send 10  stdout -auto
FI stdout
FC = 2
FP 1 /^>UPI000000000A_1_10/
FP 1 /MAETKEFKTL/
//

ID das-genedas
AP seqret
CL tgenedashuman:ENSG00000139618 -send 10 stdout -auto
FI stdout
FC = 2
FP 1 /^>ENSG00000139618/
FP 1 /^gggcttgtgg/
//

ID das-ensembldasgrch37
AP seqret
CL tensembldasgrch37:11 -sbegin 60001 -send 60010 stdout -auto
FI stdout
FC = 2
FP 1 /^>11_60001_60010/
FP 1 /^gaattctaca/
//

ID das-ensembldasservergrch37
## same as above test (das-ensembldasgrch37),
## using tensembldasserver based DB instead of directly defined dassource DB
AP seqret
CL tensembldasserver:Homo_sapiens_GRCh37_reference:11
CL -sbegin 60001 -send 60010 stdout -auto
FI stdout
FC = 2
FP 1 /^>11_60001_60010/
FP 1 /^gaattctaca/
//

###############################################################
#
# EBI webservices
#
###############################################################

ID cachedbfetch-wsdbfetch
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
CC this test can be disabled using -without=soapws option
AP cachedbfetch
CL -servername twsdbfetch -auto
CL -cachefile ~/.embossdata/qatests.server.twsdbfetch
QQ cp ~/.embossdata/qatests.server.twsdbfetch .
FI qatests.server.twsdbfetch
FP 1 /^DBNAME uniprotkb /
FP /embl/
FI stderr
FC < 173
FP 0 /Warning: non-EDAM /
FP 0 /Warning: obsolete EDAM /
//

ID cachedbfetch-ex
AP cachedbfetch
CL -servername tdbfetch -auto
CL -cachefile ~/.embossdata/qatests.server.tdbfetch
QQ cp ~/.embossdata/qatests.server.tdbfetch .
FI qatests.server.tdbfetch
FP 1 /^DBNAME uniprotkb /
FP /embl/
FI stderr
FC < 173
FP 0 /Warning: non-EDAM /
FP 0 /Warning: obsolete EDAM /
//

ID wsdbfetch-uniprot
TI 120
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP seqret
CL fasta::twsdbfetch:uniprotkb:P06213 stdout -auto
FI stdout
FC = 25
FP 1 /^>INSR_HUMAN/
FP 1 /PS$/
//

ID dbfetch-uniprot
AP seqret
CL fasta::tdbfetch:uniprotkb:P06213 stdout -auto
FI stdout
FC = 25
FP 1 /^>INSR_HUMAN/
FP 1 /PS$/
//

ID wsdbfetch-edam
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP ontoget
CL twsdbfetch:edam:0352 stdout -auto
FI stdout
FC > 10
FP /^id: EDAM_operation:0352\n/
FP /local alignment/
//

ID dbfetch-edam
AP ontoget
CL tdbfetch:edam:0352 stdout -auto
FI stdout
FC > 10
FP /^id: EDAM_operation:0352\n/
FP /local alignment/
//

ID wsdbfetch-uniprotxml
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP xmlget
CL uniprotxml::twsdbfetch:uniprotkb:p12345 stdout -auto
FI stdout
FC > 160
FP 1 /<uniprot xmlns="http://uniprot.org/uniprot"/
FP 1 /<accession>P12345</accession>/
//

ID dbfetch-uniprotxml
AP xmlget
CL uniprotxml::tdbfetch:uniprotkb:p12345 stdout -auto
FI stdout
FC > 160
FP 1 /<uniprot xmlns="http://uniprot.org/uniprot"/
FP 1 /<accession>P12345</accession>/
//

ID wsdbfetch-noentry
RQ soapws
TI 120
CC requires (axis2C) SOAP webservices library enabled
AP seqret
CL fasta::twsdbfetch:uniprotkb:abcdefg stdout -auto
ER 1
FI stderr
FC = 2
FP 1 /Unable to read sequence/
//

ID dbfetch-noentry
AP seqret
CL tdbfetch:uniprotkb:abcdefg stdout -auto
ER 1
FI stderr
FC = 2
FP 1 /Unable to read sequence/
//

ID cacheebeyesearch-ex
RQ soapws
TI 180
CC requires (axis2C) SOAP webservices library enabled
AP cacheebeyesearch
CL -cachefile ~/.embossdata/qatests.server.ebeye -auto
QQ cp ~/.embossdata/qatests.server.ebeye .
FI qatests.server.ebeye
FP 1 /^DBNAME uniprot /
//

ID ebeye-uniprot
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP textget
CL tebeye:uniprot:1A74_HUMAN stdout -auto
FI stdout
FC > 10
FP /P30459/
FP /HLA-A/
//

ID ebeye-emblrel_con-multifield
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP textget
CL "tebeye:emblrelease_con-{keywords:Aspergillus fumigatus & description:BAC}"
CL stdout -auto
FI stdout
FP /BX649216/
FP /Aspergillus fumigatus BAC pilot project supercontig/
//

ID ebeye-uniprot-multifield
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP textget
CL "ebeye:uniprot-{description:genome polyprotein & sequence_length:496}"
CL stdout -auto
FI stdout
FP /B8LSD5/
FP /Hepatitis C virus/
FP /seq.*length.*496/
FP /emblcds: ABV55385/
//

###################
# Ensembl
###################

ID cacheensembl-ex
TI 180
AP cacheensembl
CL -servername ensembl -cachefile ~/.embossdata/qatests.server.ensembl -auto
QQ cp ~/.embossdata/qatests.server.ensembl .
FI qatests.server.ensembl
FP 1 /^ALIAS 9606 homo_sapiens\n/
FP 8 /^ALIAS \S+ homo_sapiens\n/
FP 1 /^DBNAME homo_sapiens \[/
FP 6 /^DBNAME homo_sapiens/
FI stdout
FC = 140
FP 6 /homo_sapiens/
//

###################
# Main applications
###################

ID aaindexextract-keep
AP aaindexextract
DL keep
PP mkdir ./AAINDEX
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
IN ../../data/aaindex1.test
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI AAINDEX
DF kytj820101
//

ID abiview-ex
AP abiview
CL -graph cps
IN ../../data/abiview.abi
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created abiview\.ps\n/
FI abiview.fasta
FP /^>abiview\n/
FP /^GNNNNNNNNNG/
FZ = 861
FI abiview.ps
FP /^%%Title: PLplot Graph\n/
//

##ID abiview-old
##AP abiview
##CC Example file missing test/data/ba16d2.s1
##CL -graph ps
##IN ../../data/ba16d2.s1
##IN
##FI stderr
##FC = 2
##FI stdout
##FZ = 18
##FP /^Created abiview\.ps\n/
##FI outfile.fasta
##FZ = 0
##//

ID aligncopy-ex
AP aligncopy
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.aligncopy
FC = 68
FP /HBB_HUMAN          1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR     40\n/
FP /                               ::  : : :.: : : :   :::: ::   :  : :  : \n/
//

ID aligncopypair-ex
AP aligncopypair
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.aligncopypair
FC = 683
FP 21 /Aligned_sequences:/
FP /HBB_HUMAN          1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR     40\n/
//

ID antigenic-command
AP antigenic
CL tsw:amir_pseae -auto
FI amir_pseae.antigenic
FP /^# Program: antigenic\n/
FP /Sequence: AMIR_PSEAE/
FP /246/
FP /1\.246/
FP / NSLLGSL/
FZ > 100
FC > 5
//

ID antigenic-ex
AP antigenic
IN tsw:actb1_takru
IN
IN
FI actb1_takru.antigenic
FP /^# Program: antigenic\n/
FP /1\.207/
FP /AA[^AV]VV/
FZ > 100
FC > 5
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID antigenic-keep
UC By using the '-rformat gff' qualifier, a GFF file of the predicted regions can be produced.
AP antigenic
CL -rformat gff
DL keep
IN tsw:actb1_takru
IN
IN
FI actb1_takru.antigenic
FP /^##sequence-region ACTB1_TAKRU 1 375\n/
FP /^#!Type Protein\n/
FP /^ACTB1_TAKRU\tantigenic\tepitope\t214\t222\t1\.207\t\.\t\.\tID=ACTB1_TAKRU\.1;note=\*pos 218\n/
FC = 23
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID backtranambig-ex
AP backtranambig
IN tsw:opsd_human
IN
FI opsd_human.fasta
FP /^>OPSD_HUMAN/
FP /^ATGAAYGGNACNGARGGNCCNAAYTTYTAYGTNCCNTTYWSNAAYGCNACNGGNGTNGTN\n/
FP /^MGNWSNCCNTTYGARTAYCCNCARTAYTAYYTNGCNGARCCNTGGCARTTYWSNATGYTN\n/
FP /^TGGGTNATGGCNYTNGCNTGYGCNGCNCCNCCNYTNGCNGGNTGGWSNMGNTAYATHCCN\n/
FP /^GARACNWSNCARGTNGCNCCNGCN\n/
FZ = 1101
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID backtranseq-ex
UC Note that this is a human protein and so the default human codon frequency file is used ie. is not specified
AP backtranseq
IN tsw:opsd_human
IN
FI opsd_human.fasta
FP /^>OPSD_HUMAN/
FP /CGCCACCGGCGTGGTG\n/
FZ = 1101
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID backtranseq-ex2
UC This uses a drosophila sequence and codon table.
AP backtranseq
CL -cfile Edrome.cut
IN tsw:ach2_drome
IN
FI ach2_drome.fasta
FP /^>ACH2_DROME/
FP /GAGAAGAAGAAC\n/
FZ = 1832
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID backtranseq-nbrf
UC Using an NBRF format sequence
AP backtranseq
IN ../../data/104k.nbrf
IN
FI 104k_thean.fasta
FP /^>104K_THEAN/
FP /^GGCATCCTGTGA\n/
FZ = 2709
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID banana-data
AP banana
CL -outfile banana.data -nograph
IN tembl:u68037
FI banana.data
FC = 1219
FP /c      17\.7     20\.0\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID banana-ex
AP banana
CL -nooutfile -graph ps
IN tembl:u68037
FI stdout
FC = 1
FP /^Created banana\.ps\n/
FI banana.ps
FC > 1
FP /%%Title: PLplot Graph\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID banana-ex2
AP banana
CL -graph data
IN tembl:u68037
FI banana.profile
FZ = 25601
FP /^a +0\.0 +0\.0\nt +19\.7 +0\.0\ng +17\.7 +0\.0\na +21\.1 +0\.0\n/
FP /^a +14\.9 +0\.0\nc +17\.7 +20\.0\nc +15\.7 +19\.2\nt +15\.7 +18\.5\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 9
FP /^Created banana1\.dat\n/
FI banana1.dat
FC > 1
FP /^##/
FI banana2.dat
FC > 1
FP /^##/
FI banana3.dat
FC > 1
FP /^##/
FI banana4.dat
FC > 1
FP /^##/
FI banana5.dat
FC > 1
FP /^##/
FI banana6.dat
FC > 1
FP /^##/
FI banana7.dat
FC > 1
FP /^##/
FI banana8.dat
FC > 1
FP /^##/
FI banana9.dat
FC > 1
FP /^##/
//

ID biosed-ex
UC Replace all 'T's with 'U's to create an RNA sequence
AP biosed
CL tembl:x65923 x65923.rna -target T -replace U
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.rna
FZ = 563
FP /^UCUAAUAAAAAAGCCACUUAGUUCAGUCAAAAAAAAAA\n/
//

ID biosed-ex2
UC Replace all 'PPP' protein motifs with 'XXPPPXX' 
AP biosed
CL tsw:amir_pseae amir_pseae.pep -target PPP -replace XXPPPXX
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir_pseae.pep
FZ = 251
FP /^MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXESFDVPVDVV\n/
//

ID btwisted-ex
AP btwisted
CL -auto tembl:ab000095 -sbegin 100 -send 120
FI ab000095.btwisted
FP /^# Twisting calculated from 100 to 120 of AB000095\n/
FP /^Total twist \(degrees\): 681\.1\n/
FP /^Total turns : 1\.89\n/
FP /^Average bases per turn: 11\.10\n/
FP /^Total stacking energy : -179\.34\n/
FP /^Average stacking energy per dinucleotide: -8\.97\n/
//

ID cai-ex
AP cai
CL TEMBL:AB009602
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ab009602.cai
FP /0\.188/
//

ID chaos-ex
AP chaos
CL tembl:j01636 -graph cps
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI chaos.ps
FZ > 100
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI stdout
FZ = 17
FP /^Created chaos\.ps\n/
//

ID chaos-data
AP chaos
CL tembl:j01636 -graph data
FI stdout
FC = 1
FP /^Created chaos1\.dat\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI chaos1.dat
FC = 7495
FP /^##Maintitle Chaos game representation of tembl-id:J01636\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^##Screen x1 -0\.100000 y1 -0\.100000 x2 1\.400000 y2 1\.100000\n/
FP /^Line x1 0\.090456 y1 0\.242971 x2 0\.090556 y2 0\.242971 colour 0\n/
FP /^Text3 x1 0\.000000 y1 0\.000000 colour 0 size 1\.000000 A\n/
FP /^Text1 x1 1\.100000 y1 0\.750000 colour 0 size 0\.500000 A 1739\n/
FP /^Text1 x1 1\.100000 y1 0\.450000 colour 0 size 0\.500000 [%]A 23\.26\n/
//

ID charge-ex
AP charge
CL tsw:hbb_human
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hbb_human.charge
FP /CHARGE of HBB_HUMAN from 1 to 147: window 5/
FC = 146
//

ID checktrans-ex
AP checktrans
IN ../../data/paamir.pep
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI paamir_1.checktrans
FZ = 132
FP /Total STOPS:\s+7\n/
FP /^\s+7\s+635\s+357\s+278-634\s+PAAMIR_1_7\n/
FI paamir_1.fasta
FZ = 375
FP /\A>PAAMIR_1_7\n/
FP /^PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR\n/
FI paamir_1.gff
FC = 6
FP /^PAAMIR_1\t\S+\t\S+\t278\t634\t\./
//

ID chips-ex
AP chips
CL -sbeg 135 -send 1292
IN tembl:x13776
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.chips
FP /Nc = 32\.951/
//

ID cirdna-ex
AP cirdna
CL -graph cps
IN ../../data/data.cirp
IN
IN
IN
IN
FI stderr
FC = 9
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cirdna.ps
FC = 658
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI stdout
FZ = 18
FP /^Created cirdna\.ps\n/
//

ID codcmp-ex
UC This compares the codon usage tables for Escherichia coli and Haemophilus influenzae.
AP codcmp
IN Eecoli.cut
IN Ehaein.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.codcmp
FP /^Mean Squared Difference = 0\.034\n/
FP /^Sum Squared Difference = 2\.178\n/
FP /^Root Mean Squared Difference = 0\.184\n/
FP /^Sum Difference         = 9\.504\n/
FP /^Mean Difference         = 0\.14[89]\n/
FP /^Codons not appearing   = 0\n/
//

ID codcopy-ex
AP codcopy
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 75
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//

ID codcopy-outemboss
AP codcopy
DL keep
CL -oformat emboss
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.emboss
FC = 75
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//

ID codcopy-outcut
AP codcopy
DL keep
CL -oformat cut
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 75
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//

ID codcopy-outgcg
AP codcopy
DL keep
CL -oformat gcg
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.gcg
FC = 83
FP 64 /^[A-Z][a-z][a-z] +[ACGT][ACGT][ACGT]/
FP /^Asp     GAC   30454\.00      19\.05      0\.37\n/
FP /^Asp     GAT   51514\.00      32\.22      0\.63\n/
FP /^Ile     ATC   39971\.00      25\.00      0\.42\n/
FP /^Leu     CTG   84455\.00      52\.82      0\.50\n/
FP /^Met     ATG   44414\.00      27\.78      1\.00\n/
FP /^End     TAG     365\.00       0\.23      0\.07\n/
//

ID codcopy-outcutg
AP codcopy
DL keep
CL -oformat cutg
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cutg
FC = 28
FP 16 /^[ACGU][ACGU][ACGU]/
FP /^Escherichia coli K12 \[gbbct\]: 5045 CDS's \(1598893 codons\)\n/
FP /^UUG 13\.7\( 21948\)  UCG  8\.9\( 14256\)  UAG  0\.2\(   365\)  UGG 15\.3\( 24468\)\n/
FP /^CUG 52\.8\( 84455\)  CCG 23\.2\( 37150\)  CAG 28\.8\( 46100\)  CGG  5\.4\(  8619\)\n/
FP /^AUC 25\.0\( 39971\)  ACC 23\.4\( 37354\)  AAC 21\.6\( 34554\)  AGC 16\.0\( 25632\)\n/
FP /^AUG 27\.8\( 44414\)  ACG 14\.4\( 22977\)  AAG 10\.2\( 16305\)  AGG  1\.2\(  1944\)\n/
FP /^GUU 18\.4\( 29410\)  GCU 15\.4\( 24549\)  GAU 32\.2\( 51514\)  GGU 24\.8\( 39714\)\n/
FP /^GUC 15\.2\( 24336\)  GCC 25\.5\( 40761\)  GAC 19\.0\( 30454\)  GGC 29\.4\( 47013\)\n/
FP /^Coding GC 51\.81% 1st letter GC 58\.93% 2nd letter GC 40\.69% 3rd letter GC 55\.80%\n/
//

ID codcopy-outcutgaa
AP codcopy
DL keep
CL -oformat cutgaa
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cutgaa
FC = 29
FP 16 /^[ACGU][ACGU][ACGU]/
FP /^Escherichia coli K12 \[gbbct\]: 5045 CDS's \(1598893 codons\)\n/
FP /^UUG L 0\.13 13\.7 \( 21948\)  UCG S 0\.15  8\.9 \( 14256\)  UAG \* 0\.07  0\.2 \(   365\)  UGG W 1\.00 15\.3 \( 24468\)\n/
FP /^CUG L 0\.50 52\.8 \( 84455\)  CCG P 0\.52 23\.2 \( 37150\)  CAG Q 0\.65 28\.8 \( 46100\)  CGG R 0\.10  5\.4 \(  8619\)\n/
FP /^AUC I 0\.42 25\.0 \( 39971\)  ACC T 0\.4[34] 23\.4 \( 37354\)  AAC N 0\.55 21\.6 \( 34554\)  AGC S 0\.28 16\.0 \( 25632\)\n/
FP /^AUG M 1\.00 27\.8 \( 44414\)  ACG T 0\.27 14\.4 \( 22977\)  AAG K 0\.23 10\.2 \( 16305\)  AGG R 0\.02  1\.2 \(  1944\)\n/
FP /^GUU V 0\.26 18\.4 \( 29410\)  GCU A 0\.16 15\.4 \( 24549\)  GAU D 0\.63 32\.2 \( 51514\)  GGU G 0\.34 24\.8 \( 39714\)\n/
FP /^GUC V 0\.2[12] 15\.2 \( 24336\)  GCC A 0\.27 25\.5 \( 40761\)  GAC D 0\.37 19\.0 \( 30454\)  GGC G 0\.40 29\.4 \( 47013\)\n/
FP /^Coding GC 51\.81% 1st letter GC 58\.93% 2nd letter GC 40\.69% 3rd letter GC 55\.80%\n/
//

ID codcopy-outspsum
AP codcopy
DL keep
CL -oformat spsum
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.spsum
FC = 2
FP 1 /^(\d+\s+){63}\d+\n/
FP /^Escherichia coli K12: 5045\n/
FP /^.* 84455 .* 30454 51514 .* 39971 .* 44414 .* 365 .*\n/
//

ID codcopy-outcherry
AP codcopy
DL keep
CL -oformat cherry
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cherry
FC = 86
FP 64 /^[A-Z][a-z][a-z]\s+[ACGT][ACGT][ACGT]/
FP /^Escherichia coli K12\n/
FP /^5045 genes found in CUTG146\n/
FP /^Asp     GAT    51514\.00     32\.22      0\.63\n/
FP /^Asp     GAC    30454\.00     19\.05      0\.37\n/
FP /^Ile     ATC    39971\.00     25\.00      0\.42\n/
FP /^Leu     CTG    84455\.00     52\.82      0\.50\n/
FP /^Met     ATG    44414\.00     27\.78      1\.00\n/
FP /^End     TAG      365\.00      0\.23      0\.07\n/
//

ID codcopy-outtransterm
AP codcopy
DL keep
CL -oformat transterm
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.transterm
FC = 83
FP 64 /^[A-Z][a-z][a-z]\s+[ACGT][ACGT][ACGT]/
FP /^Asp     GAT    51514\.00     32\.22      0\.63\n/
FP /^Asp     GAC    30454\.00     19\.05      0\.37\n/
FP /^Met     ATG    44414\.00     27\.78      1\.00\n/
FP /^Ile     ATC    39971\.00     25\.00      0\.42\n/
FP /^End     TAG      365\.00      0\.23      0\.07\n/
FP /^Leu     CTG    84455\.00     52\.82      0\.50\n/
//

ID codcopy-outcodehop
AP codcopy
DL keep
CL -oformat codehop
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.codehop
FC = 68
FP 64 /^0\.[0-9]+\t-- \[[ 0-9][0-9]\] [ACGU][ACGU][ACGU]\n/
FP /^0\.024999\t-- \[13\] AUC\n/
FP /^0\.027778\t-- \[14\] AUG\n/
FP /^0\.052821\t-- \[30\] CUG\n/
FP /^0\.019047\t-- \[33\] GAC\n/
FP /^0\.032219\t-- \[35\] GAU\n/
FP /^0\.000228\t-- \[50\] UAG\n/
FP /^Eecoli\.cut\n/
FP /^Codon usage for Escherichia coli K12: 5045\n/
FP /^ from CUTG146\/gbbct: 1598893 codons\n/
//

ID codcopy-outstaden
AP codcopy
DL keep
CL -oformat staden
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.staden
FC = 21
FP 16 /^\s+[A-Z] [ACGT][ACGT][ACGT]/
FP /^      L TTG 21948 S TCG 14256 \* TAG  365 W TGG 24468\n/
FP /^      L CTG 84455 P CCG 37150 Q CAG 46100 R CGG 8619\n/
FP /^      I ATC 39971 T ACC 37354 N AAC 34554 S AGC 25632\n/
FP /^      M ATG 44414 T ACG 22977 K AAG 16305 R AGG 1944\n/
FP /^      V GTT 29410 A GCT 24549 D GAT 51514 G GGT 39714\n/
FP /^      V GTC 24336 A GCC 40761 D GAC 30454 G GGC 47013\n/
//


ID codcopy-outnumstaden
AP codcopy
DL keep
CL -oformat numstaden
IN Eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.numstaden
FC = 21
FP 16 /^\s+[A-Z] [ACGT][ACGT][ACGT]/
FP /^      L TTG 21948 S TCG 14256 \* TAG  365 W TGG 24468\n/
FP /^      L CTG 84455 P CCG 37150 Q CAG 46100 R CGG 8619\n/
FP /^      I ATC 39971 T ACC 37354 N AAC 34554 S AGC 25632\n/
FP /^      M ATG 44414 T ACG 22977 K AAG 16305 R AGG 1944\n/
FP /^      V GTT 29410 A GCT 24549 D GAT 51514 G GGT 39714\n/
FP /^      V GTC 24336 A GCC 40761 D GAC 30454 G GGC 47013\n/
//


ID codcopy-emboss
AP codcopy
CL -format emboss
IN ../codcopy-outemboss/eecoli.emboss
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 75
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//


ID codcopy-cut
AP codcopy
CL -format cut
IN ../codcopy-outcut/eecoli.cut
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 75
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//


ID codcopy-gcg
AP codcopy
CL -format gcg
IN ../codcopy-outgcg/eecoli.gcg
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 72
FP 64 /^[ACGT][ACGT][ACGT]/
FP 0 /Escherichia/
FP 0 /gbbct/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.370    19\.050  30454\n/
FP /^GAT    D     0\.630    32\.220  51514\n/
FP /^ATC    I     0\.420    25\.000  39971\n/
FP /^CTG    L     0\.500    52\.820  84455\n/
FP /^ATG    M     1\.000    27\.780  44414\n/
FP /^TAG    \*     0\.070     0\.230    365\n/
//


ID codcopy-cutg
AP codcopy
CL -format cutg
IN ../codcopy-outcutg/eecoli.cutg
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 74
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.000  30454\n/
FP /^GAT    D     0\.628    32\.200  51514\n/
FP /^ATC    I     0\.419    25\.000  39971\n/
FP /^CTG    L     0\.496    52\.800  84455\n/
FP /^ATG    M     1\.000    27\.800  44414\n/
FP /^TAG    \*     0\.072     0\.200    365\n/
//


ID codcopy-cutgaa
AP codcopy
CL -format cutgaa
IN ../codcopy-outcutgaa/eecoli.cutgaa
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 74
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.370    19\.000  30454\n/
FP /^GAT    D     0\.630    32\.200  51514\n/
FP /^ATC    I     0\.420    25\.000  39971\n/
FP /^CTG    L     0\.500    52\.800  84455\n/
FP /^ATG    M     1\.000    27\.800  44414\n/
FP /^TAG    \*     0\.070     0\.200    365\n/
//


ID codcopy-spsum
AP codcopy
CL -format spsum
IN ../codcopy-outspsum/eecoli.spsum
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 73
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP 0 /gbbct/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//


ID codcopy-cherry
AP codcopy
CL -format cherry
IN ../codcopy-outcherry/eecoli.cherry
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 74
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP 0 /gbbct/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.370    19\.050  30454\n/
FP /^GAT    D     0\.630    32\.220  51514\n/
FP /^ATC    I     0\.420    25\.000  39971\n/
FP /^CTG    L     0\.500    52\.820  84455\n/
FP /^ATG    M     1\.000    27\.780  44414\n/
FP /^TAG    \*     0\.070     0\.230    365\n/
//


ID codcopy-transterm
AP codcopy
CL -format transterm
IN ../codcopy-outtransterm/eecoli.transterm
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 72
FP 64 /^[ACGT][ACGT][ACGT]/
FP 0 /Escherichia/
FP 0 /gbbct/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.370    19\.050  30454\n/
FP /^GAT    D     0\.630    32\.220  51514\n/
FP /^ATC    I     0\.420    25\.000  39971\n/
FP /^CTG    L     0\.500    52\.820  84455\n/
FP /^ATG    M     1\.000    27\.780  44414\n/
FP /^TAG    \*     0\.070     0\.230    365\n/
//


ID codcopy-codehop
AP codcopy
CL -format codehop
IN ../codcopy-outcodehop/eecoli.codehop
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 75
FP 64 /^[ACGT][ACGT][ACGT]/
FP /^#Species: Escherichia coli K12\n/
FP /^#Division: gbbct\n/
FP /^#Release: CUTG146\n/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39970\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    364\n/
//


ID codcopy-staden
AP codcopy
CL -format staden
IN ../codcopy-outstaden/eecoli.staden
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 72
FP 64 /^[ACGT][ACGT][ACGT]/
FP 0 /Escherichia/
FP 0 /gbbct/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//


ID codcopy-numstaden
AP codcopy
CL -format numstaden
IN ../codcopy-outnumstaden/eecoli.numstaden
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI eecoli.cut
FC = 72
FP 64 /^[ACGT][ACGT][ACGT]/
FP 0 /Escherichia/
FP 0 /gbbct/
FP 0 /CUTG146/
FP /^#CdsCount: 5045\n/
FP /^#Coding GC 51\.81%\n/
FP /^#1st letter GC 58\.93%\n/
FP /^#2nd letter GC 40\.69%\n/
FP /^#3rd letter GC 55\.80%\n/
FP /^GAC    D     0\.372    19\.047  30454\n/
FP /^GAT    D     0\.628    32\.219  51514\n/
FP /^ATC    I     0\.419    24\.999  39971\n/
FP /^CTG    L     0\.496    52\.821  84455\n/
FP /^ATG    M     1\.000    27\.778  44414\n/
FP /^TAG    \*     0\.072     0\.228    365\n/
//


ID coderet-ex
UC To extract all of the CDS, mRNA, non-coding and the protein translations:
AP coderet
IN tembl:x03487
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x03487.cds
FP /^>x03487_cds_1\natgacgaccgcgt/
FI x03487.mrna
FP /^>x03487_mrna_1\ncagacgttcttcgccgagagtcgtcggggttt/
FI x03487.prot
FP /^>x03487_pro_1\nMTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMS/
FI x03487.noncoding
FP /^>x03487_noncoding_501\ngtgagcgcgggc/
FI x03487.coderet
FC = 3
FP /     1     1     6     1     8 X03487\n/
//

ID coderet-ex2
UC To only extract the mRNA sequence:
AP coderet
CL -nocds -notranslation -norest
IN tembl:X03487
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x03487.mrna
FP /^>x03487_mrna_1\ncagacgttcttcgccgagagtcgtcggggttt/
FI x03487.coderet
FC = 3
FP /     1     1 X03487\n/
//

ID compseq-ex
UC To count the frequencies of dinucleotides in a file:
AP compseq
CL tembl:x65923 -word 2 result3.comp
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI result3.comp
FZ = 913
FP /^Total count\s+517\n/
FP /^AA\s+45\s+0\.0870406\s+0\.0625000\s+1\.3926499\n/
//

ID compseq-ex2
UC To count the frequencies of hexanucleotides, without outputting the results of hexanucleotides that do not occur in the sequence:
AP compseq
CL tembl:x65923 -word 6 result6.comp -nozero
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI result6.comp
FZ = 18690
FP /^Total count\s+513\n/
FP /^AAAAAA\s+6\s+0\.0116959\s+0\.0002441\s+47\.9064327\n/
//

ID compseq-ex3
UC To count the frequencies of trinucleotides in frame 2 of a sequence and use a previously prepared compseq output to show the expected frequencies:
AP compseq
CL tembl:x65923 -word 3 result3.comp -frame 2 -in ../../data/prev.comp
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI result3.comp
FZ = 2698
FP /^Total count\s+172\n/
FP /^AAA\s+7\s+0\.0406977\s+0\.0329457\s+1\.2352955\n/
//

ID cons-ex
AP cons
IN ../../data/dna.msf
IN aligned.cons
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FC = 2
FI aligned.cons
FZ = 134
FP /\A>EMBOSS_001\n/
FP 2 /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID consambig-ex
AP consambig
IN ../../data/dna.msf
IN aligned.consambig
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FC = 2
FI aligned.consambig
FZ = 134
FP /\A>EMBOSS_001\n/
FP /^ACGTACGTACGTACGTACGTacgtACGTACGTACGTACGTMSKWMSKWMSKWMSKWMSKW\n/
FP /^MSKWMSKWMSKWMSKWMSKWACGTACGTACGTACGTACGTACGTACGTWSSWACGTACGT\n/
//

ID cpgplot-ex
AP cpgplot
CL tembl:u68037 -graph cps
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created cpgplot\.ps\n/
FI u68037.cpgplot
FP /U68037 from 1 to 1218/
FP /Observed\/Expected ratio > 0\.60/
FP /Length 406 \(104\.\.509\)/
FP /Length 329 \(596\.\.924\)/
FI u68037.gff
FP /^#!Type DNA\n/
FP /^##sequence-region U68037 1 924\n/
FI cpgplot.ps
FP /^%%Title: PLplot Graph/
//

ID cpgplot-old
AP cpgplot
CL tembl:u68037 -graph data
IN
IN
IN
IN
IN
IN
FI stdout
FC = 3
FP /^Created cpgplot3\.dat\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI u68037.cpgplot
FP /U68037 from 1 to 1218/
FP /Observed\/Expected ratio > 0\.60/
FP /Length 406 \(104\.\.509\)/
FP /Length 329 \(596\.\.924\)/
FI u68037.gff
FC = 7
FP /^U68037\t\S+\t\S+\t104\t509\t/
FP /^U68037\t\S+\t\S+\t596\t924\t/
FI cpgplot1.dat
FZ = 24865
FP /^444\.000000\s+1\.066856\n/
FI cpgplot2.dat
FZ = 25979
FP /^444\.000000\s+75\.000000\n/
FI cpgplot3.dat
FZ = 24863
FP /^444\.000000\s+1\.000000\n/
//

ID cpgreport-ex
AP cpgreport
CL tembl:u68037
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI u68037.cpgreport
FP /CPGREPORT of U68037 from 1 to 1218/
FP /U68037                   12     13    17          1 100\.0    -/
FP /U68037                 1183   1193    26          2  72\.7   2\.00/
FI u68037.gff
FC = 11
FP /^U68037\tcpgreport\tsequence_feature\t96\t1032\t630\t/
//

ID cusp-ex
UC This example uses only one input sequence.
UC The normal use would be to use a set of coding sequences as the input.
AP cusp
CL -sbeg 135 -send 1292
IN tembl:x13776
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.cusp
FP /GCA +A +0\.077 +7\.772 +3/
FP /GCC +A +0\.462 +46\.632 +18/
FP /GCG +A +0\.462 +46\.632 +18/
FP /GCT +A +0\.000 +0\.000 +0/
//

ID cutgextract-keep
AP cutgextract
DL keep
PP mkdir CODONS
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
IN ../../data
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI CODONS
FI outfile.cutgextract
FC = 9
FP 9 /^Writing .*\.cut/
//

ID cutgextract-species
AP cutgextract
DL keep
PP mkdir CODONS
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
CL -species "Aedes *"
IN ../../data
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI CODONS
FI outfile.cutgextract
FC = 3
FP 3 /^Writing .*\.cut/
//

ID cutgextract-outfile
AP cutgextract
DL keep
PP mkdir CODONS
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
CL -species "Aedes *" -filename EAedes
IN ../../data
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI CODONS
FI outfile.cutgextract
FC = 1
FP 1 /^Writing EAedes\.cut/
//

ID cutseq-ex
UC To remove bases 10 to 12 from a database entry and write to the new sequence file 'gatta2.seq':
AP cutseq
CL tembl:x13776 gatta2.seq -from=10 -to=12
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI gatta2.seq
FZ = 2293
FP /^ggtaccgctcgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgatcta\n/
//

ID cutseq-ex2
UC To remove the first 20 bases from 'tembl:x13776' and write it to 'jsh.seq': 
AP cutseq
CL tembl:x13776 -from=1 -to=20 -out=jsh.seq
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI jsh.seq
FZ = 2275
FP /^tgctcgatcaccaccagccgggcgacgggaactgcacgatctacctggcgagcctggagc\n/
//

ID cutseq-ex3
UC If the default start and end positions are accepted, then all of the sequence is removed!
AP cutseq
CL tembl:x13776 starta.seq -sbeg=-1000 -send=1290
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI starta.seq
FZ = 92
FP /\A>X13776 X13776\.1 .* regulation\Z/
//

ID dan-ex
AP dan
IN tembl:x13776
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.dan
FC = 2167
FP / +1 +20 +[+] +64\.9 +70\.0 .* ggtaccgctggccgagcatc *\n/
FP / +2 +21 +[+] +63\.7 +65\.0 .* gtaccgctggccgagcatct *\n/
//

ID dan-ex2
UC An example of producing a plot of Tm:
AP dan
CL -plot -graph cps
IN tembl:x13776
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 15
FP /^Created dan\.ps\n/
FI dan.ps
FP /^%%Title: PLplot Graph/
//

ID dan-old
UC An example of producing a plot of Tm:
AP dan
CL -plot -graph data
IN tembl:x13776
IN
IN
IN
IN
IN
FI stdout
FC = 1
FP /^Created dan1\.dat\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI dan1.dat
FZ = 46589
FP /^11\.000000\s+64\.921204\n/
FP /^2158\.000000\s+62\.373310\n/
//

ID density-ex
AP density
CL tembl:x13776
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.density
FC = 2095
FP / +1 +1 +[+] +0\.000  0\.180  0\.330  0\.330  0\.160  0\.340  0\.660\n/
//

ID density-ex2
AP density
CL tembl:x13776 -display quad -graph cps
FI stdout
FC = 1
FP /^Created density\.ps\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI density.ps
FP /^%%Title: PLplot Graph/
//

ID density-ex3
AP density
CL tembl:x13776 -display dual -graph cps
FI stdout
FC = 1
FP /^Created density\.ps\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI density.ps
FP /^%%Title: PLplot Graph/
//

#############################################
# Direct access database(s)
#############################################

ID direct-all
AP seqret
CL "temblall:*" test.out -auto
FI test.out
FP 52 /^>/
//

ID direct-filename
AP seqret
CL "temblvrt:*" test.out -auto
FI test.out
FP 31 /^>/
//

ID direct-exclude
AP seqret
CL "temblrest:*" test.out -auto
FI test.out
FP 21 /^>/
//

#############################################
# The qapblast database(s)
#############################################

ID dbiblast-allsys-keep
DL keep
AP dbiblast
CL -fields "acc,sv,des"
IN swnew
IN ../../data
IN
IN
IN
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000swnew\.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI des.hit
FZ = 576
FP s /\A.{300}\006/
FI des.trg
FZ = 1839
FP s /\A.{308}1\000/
FI seqvn.hit
FZ = 300
FP s /\A.{300}$/
FI seqvn.trg
FZ = 300
FP s /\A.{300}$/
FI outfile.dbiblast
FC = 39
FP 1 /^filename: /
FP /# Fields: 4\n/
FP /# Files: 1\n/
FP /#   File 1: .*\/data[\/\\]swnew\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Index sv: maxlen 0 items 0\n/
FP /Index des: maxlen 19 items 57\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-allnosys-keep
DL keep
AP dbiblast
CL -fields "acc,sv,des" -nosystemsort
IN swnew
IN ../../data
IN
IN
IN
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000swnew.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI des.hit
FZ = 576
FP s /\A.{300}\006/
FI des.trg
FZ = 1839
FP s /\A.{308}1\000/
FI seqvn.hit
FZ = 300
FP s /\A.{300}$/
FI seqvn.trg
FZ = 300
FP s /\A.{300}$/
FI outfile.dbiblast
FC = 40
FP 1 /^filename: /
FP /# Fields: 4\n/
FP /# Files: 1\n/
FP /#   File 1: .*\/data[\/\\]swnew\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Index sv: maxlen 0 items 0\n/
FP /Index des: maxlen 19 items 57\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-nosys-keep
DL keep
AP dbiblast
CL -nosystemsort
IN swnew
IN ../../data
IN
IN
IN
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000swnew.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI outfile.dbiblast
FC = 33
FP 1 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 1\n/
FP /#   File 1: .*\/data[\/\\]swnew\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-ex-keep
UC This creates EMBOSS indices for the BLAST database 'swnew'
DL keep
AP dbiblast
IN swnew
IN ../../data
IN
IN
IN
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000swnew.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI outfile.dbiblast
FC = 32
FP 1 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 1\n/
FP /#   File 1: .*\/data[\/\\]swnew\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-idfirst
AP seqret
CL qapblast-id:CO9_FUGRU test.out -auto
FI test.out
FZ = 649
FP 1 /^>CO9_FUGRU /
FP 1 /^>/
//

ID dbiblast-idsecond
AP seqret
CL qapblast-id:E2BB_FUGRU test.out -auto
FI test.out
FZ = 473
FP 1 /^>E2BB_FUGRU /
FP 1 /^>/
//

ID dbiblast-last
AP seqret
CL qapblast-id:TM21_FUGRU test.out -auto
FI test.out
FZ = 287
FP 1 /^>TM21_FUGRU /
FP 1 /^>/
//

ID dbiblast-nextlast
AP seqret
CL qapblast-id:ODO2_FUGRU test.out -auto
FI test.out
FZ = 569
FP 1 /^>ODO2_FUGRU /
FP 1 /^>/
//

ID dbiblast-acfirst
AP seqret
CL qapblast-acc:P53450 test.out -auto
FI test.out
FZ = 435
FP 1 /^>FOS_FUGRU P53450 /
FP 1 /^>/
//

ID dbiblast-acsecond
AP seqret
CL qapblast-acc:P79755 test.out -auto
FI test.out
FZ = 649
FP 1 /^>CO9_FUGRU P79755 /
FP 1 /^>/
//

ID dbiblast-aclast
AP seqret
CL qapblast-acc:Q90515 test.out -auto
FI test.out
FZ = 287
FP 1 /^>TM21_FUGRU Q90515 /
FP 1 /^>/
//

ID dbiblast-all
AP seqret
CL "qapblast:*" test.out -auto
FI test.out
FZ = 4474
FP 1 /^>TM21_FUGRU Q90515 /
FP 9 /^>/
//

ID dbiblast-wild
AP seqret
CL "qapblast:n*" test.out -auto
FI test.out
FZ = 516
FP 2 /^>N/
FP 2 /^>/
//

#############################################
# The qapblastsplit database(s)
#############################################

ID dbiblast-split-keep
DL keep
AP dbiblast
IN swsplit
IN ../../data
IN swsplit.*.pin
IN
IN
IN P
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 410
FP s /\A.{300}\001\000swsplit\.00\.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI outfile.dbiblast
FC = 50
FP 5 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 5\n/
FP /#   File 1: .*\/data[\/\\]swsplit\.00\.pin\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Total 5 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-split-wild-keep
DL keep
AP dbiblast
IN swsplit
IN ../../data
IN swsplit.*.*
IN
IN
IN P
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 410
FP s /\A.{300}\001\000swsplit\.00\.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI outfile.dbiblast
FC = 60
FP 5 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 15\n/
FP /#   File \d+: .*\/data[\/\\]swsplit\.00\.pin\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Total 5 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-split-list-keep
DL keep
AP dbiblast
IN swsplit
IN ../../data
IN swsplit.00.pin swsplit.01.pin swsplit.02.pin swsplit.03.pin swsplit.04.pin 
IN
IN
IN P
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 410
FP s /\A.{300}\001\000swsplit\.00\.pin\000/
FI entrynam.idx
FZ = 480
FP s /\A.{300}CO9_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\006/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42493\001/
FI outfile.dbiblast
FC = 50
FP 5 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 5\n/
FP /#   File \d+: .*\/data[\/\\]swsplit\.00\.pin\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Total 5 files 9 entries \(0 duplicates\)\n/
//

ID dbiblast-split-idfirst
AP seqret
CL qapblastsplit-id:CO9_FUGRU test.out -auto
FI test.out
FZ = 649
FP 1 /^>CO9_FUGRU /
FP 1 /^>/
//

ID dbiblast-split-idsecond
AP seqret
CL qapblastsplit-id:E2BB_FUGRU test.out -auto
FI test.out
FZ = 473
FP 1 /^>E2BB_FUGRU /
FP 1 /^>/
//

ID dbiblast-split-last
AP seqret
CL qapblastsplit-id:TM21_FUGRU test.out -auto
FI test.out
FZ = 287
FP 1 /^>TM21_FUGRU /
FP 1 /^>/
//

ID dbiblast-split-nextlast
AP seqret
CL qapblastsplit-id:ODO2_FUGRU test.out -auto
FI test.out
FZ = 569
FP 1 /^>ODO2_FUGRU /
FP 1 /^>/
//

ID dbiblast-split-acfirst
AP seqret
CL qapblastsplit-acc:P53450 test.out -auto
FI test.out
FZ = 435
FP 1 /^>FOS_FUGRU P53450 /
FP 1 /^>/
//

ID dbiblast-split-acsecond
AP seqret
CL qapblastsplit-acc:P79755 test.out -auto
FI test.out
FZ = 649
FP 1 /^>CO9_FUGRU P79755 /
FP 1 /^>/
//

ID dbiblast-split-aclast
AP seqret
CL qapblastsplit-acc:Q90515 test.out -auto
FI test.out
FZ = 287
FP 1 /^>TM21_FUGRU Q90515 /
FP 1 /^>/
//

ID dbiblast-split-all
AP seqret
CL "qapblastsplit:*" test.out -auto
FI test.out
FZ = 4474
FP 1 /^>TM21_FUGRU Q90515 /
FP 9 /^>/
//

ID dbiblast-split-wild
AP seqret
CL "qapblastsplit:n*" test.out -auto
FI test.out
FZ = 516
FP 2 /^>N/
FP 2 /^>/
//

ID dbiblast-split-testexc
AP seqret
CL qapblastsplitexc:CO9_FUGRU test.out -auto
FI test.out
FZ = 649
FP 1 /^>CO9_FUGRU /
FP 1 /^>/
//

ID dbiblast-split-testexcall
AP seqret
CL "qapblastsplitexc:*" test.out -auto
FI test.out
FZ = 3864
FP 1 /^>CO9_FUGRU /
FP 7 /^>/
//

ID dbiblast-split-testexcfail
ER 1
AP seqret
CL qapblastsplitexc:FABP_FUGRU test.out -auto
FI stderr
FZ = 131
FP /Error: Unable to read sequence 'qapblastsplitexc:FABP_FUGRU'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbiblast-split-testinc
AP seqret
CL qapblastsplitinc:FABP_FUGRU test.out -auto
FI test.out
FZ = 175
FP 1 /^>FABP_FUGRU /
FP 1 /^>/
//

ID dbiblast-split-testincall
AP seqret
CL "qapblastsplitinc:*" test.out -auto
FI test.out
FZ = 610
FP 1 /^>FABP_FUGRU /
FP 2 /^>/
//

ID dbiblast-split-testincfail
ER 1
AP seqret
CL qapblastsplitinc:CO9_FUGRU test.out -auto
FI stderr
FZ = 130
FP /Error: Unable to read sequence 'qapblastsplitinc:CO9_FUGRU'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

#############################################
# The qanfasta database
#############################################

ID dbifasta-ex-keep
DL keep
AP dbifasta
IN EMROD
IN idacc
IN ../../data
IN emrod
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp binary
FZ = 322
FP s /\A.{300}\001\000emrod\000/
FI entrynam.idx binary
FZ = 396
FP s /\A.{300}L48662\000/
FI acnum.hit binary
FZ = 324
FP s /\A.{300}\001/
FI acnum.trg binary
FZ = 384
FP s /\A.{308}L48662\001/
FI outfile.dbifasta
FC = 34
FP /^# Fields: 2\n/
FP /^#   Field 2: acc\n/
FP /^#   File 1: \S+\/data[\/\\]emrod\n/
FP /^filename: 'emrod'\n/
FP 1 /^filename: /
FP /^    id: 6\n/
FP /^   acc: 6\n/
FP /^Index acc: maxlen 6 items 6\n/
FP /^Total 1 files 6 entries \(0 duplicates\)\n/
//

ID dbifasta-allsys-keep
DL keep
AP dbifasta
CL -fields "acc,sv,des"
IN EMROD
IN idacc
IN ../../data
IN emrod
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000emrod\000/
FI entrynam.idx
FZ = 396
FP s /\A.{300}L48662\000/
FI acnum.hit
FZ = 324
FP s /\A.{300}\001/
FI acnum.trg
FZ = 384
FP s /\A.{308}L48662\001/
FI seqvn.hit
FZ = 300
FP s /\A.{44} +/
FI seqvn.trg
FZ = 300
FP s /\A.{44} +/
FI des.hit
FZ = 580
FP s /\A.{300}\001/
FP s /\A.{44} +/
FI des.trg
FZ = 1140
FP s /\A.{308}1\000/
FP s /\A.{44} +/
FI outfile.dbifasta
FC = 41
FP /^# Fields: 4\n/
FP /^#   Field 2: acc\n/
FP /^#   File 1: \S+\/data[\/\\]emrod\n/
FP /^filename: 'emrod'\n/
FP 1 /^filename: /
FP /^    id: 6\n/
FP /^   acc: 6\n/
FP /^    sv: 0\n/
FP /^   des: 71\n/
FP /^Index acc: maxlen 6 items 6\n/
FP /^Index sv: maxlen 0 items 0\n/
FP /^Index des: maxlen 13 items 40\n/
FP /^Total 1 files 6 entries \(0 duplicates\)\n/
//

ID dbifasta-allnosys-keep
DL keep
AP dbifasta
CL -fields "acc,sv,des" -nosystemsort
IN EMROD
IN idacc
IN ../../data
IN emrod
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp binary
FZ = 322
FP s /\A.{300}\001\000emrod\000/
FI entrynam.idx binary
FZ = 396
FP s /\A.{300}L48662\000/
FI acnum.hit binary
FZ = 324
FP s /\A.{300}\001/
FI acnum.trg binary
FZ = 384
FP s /\A.{308}L48662\001/
FI seqvn.hit binary
FZ = 300
FP s /\A.{44} +/
FI seqvn.trg binary
FZ = 300
FP s /\A.{44} +/
FI des.hit binary
FZ = 580
FP s /\A.{300}\001/
FP s /\A.{44} +/
FI des.trg binary
FZ = 1140
FP s /\A.{308}1\000/
FP s /\A.{44} +/
FI outfile.dbifasta
FC = 42
FP /^# Fields: 4\n/
FP /^#   Field 2: acc\n/
FP /^#   File 1: \S+\/data[\/\\]emrod\n/
FP /^filename: 'emrod'\n/
FP 1 /^filename: /
FP /^    id: 6\n/
FP /^   acc: 6\n/
FP /^    sv: 0\n/
FP /^   des: 71\n/
FP /^Index acc: maxlen 6 items 6\n/
FP /^Index sv: maxlen 0 items 0\n/
FP /^Index des: maxlen 13 items 40\n/
FP /^Total 1 files 6 entries \(0 duplicates\)\n/
//

ID dbifasta-idfirst
AP seqret
CL qanfasta-id:L48662 test.out -auto
FI test.out
FZ = 475
FP 1 /^>L48662 /
FP 1 /^>/
//

ID dbifasta-idsecond
AP seqret
CL qanfasta-id:M11903 test.out -auto
FI test.out
FZ = 861
FP 1 /^>M11903 /
FP 1 /^>/
//

ID dbifasta-last
AP seqret
CL qanfasta-id:Z46957 test.out -auto
FI test.out
FZ = 1568
FP 1 /^>Z46957 /
FP 1 /^>/
//

ID dbifasta-nextlast
AP seqret
CL qanfasta-id:U68037 test.out -auto
FI test.out
FZ = 1318
FP 1 /^>U68037 /
FP 1 /^>/
//

ID dbifasta-all
AP seqret
CL "qanfasta:*" test.out -auto
FI test.out
FZ = 5586
FP 1 /^>U68037 /
FP 6 /^>/
//

ID dbifasta-wild
AP seqret
CL "qanfasta:m*" test.out -auto
FI test.out
FZ = 2225
FP 1 /^>M11903 /
FP 3 /^>M1190/
FP 3 /^>/
//

#############################################
# The qapfasta database
#############################################

ID dbifasta-swiss-keep
DL keep
AP dbifasta
IN SWNEW
IN idacc
IN ../../data
IN swnew
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000swnew\000/
FI entrynam.idx
FZ = 498
FP s /\A.{300}O42495_FUGRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\001/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42495\001/
FI outfile.dbifasta
FC = 34
FP /# Fields: 2\n/
FP /# Files: 1\n/
FP /#   File 1: \S+\/data[\/\\]swnew\n/
FP 1 /^filename: /
FP /Index acc: maxlen 6 items 9\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
//

ID dbifasta-swiss-idfirst
AP seqret
CL qapfasta-id:O42495_FUGRU test.out -auto
FI test.out
FZ = 470
FP 1 /^>O42495_FUGRU /
FP 1 /^>/
//

ID dbifasta-swiss-idsecond
AP seqret
CL qapfasta-id:Q1KKT3_FUGRU test.out -auto
FI test.out
FZ = 465
FP 1 /^>Q1KKT3_FUGRU /
FP 1 /^>/
//

ID dbifasta-swiss-last
AP seqret
CL qapfasta-id:Q68HA9_FUGRU test.out -auto
FI test.out
FZ = 678
FP 1 /^>Q68HA9_FUGRU /
FP 1 /^>/
//

ID dbifasta-swiss-nextlast
AP seqret
CL qapfasta-id:Q50J40_FUGRU test.out -auto
FI test.out
FZ = 440
FP 1 /^>Q50J40_FUGRU /
FP 1 /^>/
//

ID dbifasta-swiss-all
AP seqret
CL "qapfasta:*" test.out -auto
FI test.out
FZ = 4654
FP 1 /^>Q2KT90_FUGRU /
FP 9 /^>/
//

ID dbifasta-swiss-wild
AP seqret
CL "qapfasta:q2*" test.out -auto
FI test.out
FZ = 960
FP 1 /^>Q2KT90_FUGRU /
FP 3 /^>Q2/
FP 3 /^>/
//

#############################################
# The qawfasta database
#############################################

ID dbifasta-worm-keep
DL keep
AP dbifasta
IN WORM
IN simple
IN ../../data
IN wormpep.clone.*
IN
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 344
FP s /\A.{300}\001\000wormpep\.clone\.AB\000/
FI entrynam.idx
FZ = 1488
FP s /\A.{300}AC3\.1\000/
FI acnum.hit
FZ = 564
FP s /\A.{300}\001/
FI acnum.trg
FZ = 1356
## Pattern needs 's' modifier ... binary data includes a newline
FP s /\A.{308}AC3\.1\000/
FI outfile.dbifasta
FC = 38
FP /# Fields: 2\n/
FP /# Files: 2\n/
FP 2 /^filename: /
FP /Index acc: maxlen 8 items 66\n/
FP /Total 2 files 66 entries \(0 duplicates\)\n/
//

ID dbifasta-worm-idfirst
AP seqret
CL qawfasta-id:AC3.1 test.out -auto
FI test.out
FZ = 426
FP 1 /^>AC3\.1 /
FP 1 /^>/
//

ID dbifasta-worm-idsecond
AP seqret
CL qawfasta-id:AC3.2 test.out -auto
FI test.out
FZ = 1057
FP 1 /^>AC3\.2 /
FP 1 /^>/
//

ID dbifasta-worm-last
AP seqret
CL qawfasta-id:ZK637.15 test.out -auto
FI test.out
FZ = 205
FP 1 /^>ZK637\.15 /
FP 1 /^>/
//

ID dbifasta-worm-nextlast
AP seqret
CL qawfasta-id:zk637.14 test.out -auto
FI test.out
FZ = 260
FP 1 /^>ZK637\.14 /
FP 1 /^>/
//

ID dbifasta-worm-all
AP seqret
CL "qawfasta:*" test.out -auto
FI test.out
FZ = 33816
FP 66 /^>/
//

ID dbifasta-worm-wild
AP seqret
CL "qawfasta:a*" test.out -auto
FI test.out
FZ = 19764
FP 40 /^>A[^\n]+\n[^>]/
FP 40 /^>/
//

ID dbifasta-worm-wildz
AP seqret
CL "qawfasta:z*" test.out -auto
FI test.out
FZ = 7264
FP 15 /^>Z[^\n]+\n[^>]/
FP 15 /^>/
//

#############################################
# The qanflat database
#############################################

ID dbiflat-ex-keep
DL keep
AP dbiflat
IN EMBL
IN EMBL
IN ../../embl
IN rod.dat
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000rod\.dat\000/
FI entrynam.idx
FZ = 396
FP s /\A.{300}L48662\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\001/
FI acnum.trg
FZ = 398
FP s /\A.{308}L48662\001/
FI outfile.dbiflat
FC = 34
FP /# Release: 0\.0\n/
FP /# Date: [0-9][0-9]\/[0-9][0-9]\/[0-9][0-9]\n/
FP /# Files: 1\n/
FP /#   File 1: .*[\/\\]rod\.dat\n/
FP /# Fields: 2\n/
FP /# Rundate: [A-Z][a-z][a-z] \d+ [A-Z][a-z][a-z] 20[0-9][0-9] 12:00:00\n/
FP 1 /^Index \S+ maxlen \d+ items \d+\n/
FP 1 /^filename: /
//

ID dbiflat-nosys-keep
DL keep
AP dbiflat
CL -nosystemsort
IN EMBL
IN EMBL
IN ../../embl
IN rod.dat
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000rod\.dat\000/
FI entrynam.idx
FZ = 396
FP s /\A.{300}L48662\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\001/
FI acnum.trg
FZ = 398
FP s /\A.{308}L48662\001/
FI outfile.dbiflat
FC = 35
FP /# Release: 0\.0\n/
FP /# Date: \d\d\/\d\d\/[0-9][0-9]\n/
FP /# Files: 1\n/
FP /#   File 1: .*[\/\\]rod\.dat\n/
FP /# Fields: 2\n/
FP /# Rundate: [A-Z][a-z][a-z] \d\d [A-Z][a-z][a-z] 20[0-9][0-9] 12:00:00\n/
FP 1 /^Index \S+ maxlen \d+ items \d+\n/
FP 1 /^filename: /
//

ID dbiflat-id
AP seqret
CL qanflat-id:M11905 test.out -auto
FI test.out
FZ = 654
FP /\A>M11905 /
FP 1 /^>/
//

ID dbiflat-idfirst
AP seqret
CL qanflat-id:L48662 test.out -auto
FI test.out
FZ = 475
FP 1 /^>L48662 /
FP 1 /^>/
//

ID dbiflat-idsecond
AP seqret
CL qanflat-id:M11903 test.out -auto
FI test.out
FZ = 861
FP 1 /^>M11903 /
FP 1 /^>/
//

ID dbiflat-last
AP seqret
CL qanflat-id:Z46957 test.out -auto
FI test.out
FZ = 1568
FP 1 /^>Z46957 /
FP 1 /^>/
//

ID dbiflat-nextlast
AP seqret
CL qanflat-id:U68037 test.out -auto
FI test.out
FZ = 1318
FP 1 /^>U68037 /
FP 1 /^>/
//

ID dbiflat-all
AP seqret
CL "qanflat:*" test.out -auto
FI test.out
FZ = 5586
FP 1 /^>L48662 /
FP 6 /^>/
//

ID dbiflat-wild
AP seqret
CL "qanflat:*7" test.out -auto
FI test.out
FZ = 2886
FP 1 /^>Z46957 /
FP 2 /^>/
//

ID dbiflat-wild2
AP seqret
CL "qanflat:m119*" test.out -auto
FI test.out
FZ = 2225
FP 1 /^>M11904 /
FP 3 /^>/
//

ID dbiflat-tembl-idfirst
AP seqret
CL tembl-id:AB000095 test.out -auto
FI test.out
FZ = 2542
FP 1 /^>AB000095 /
FP 1 /^>/
//

ID dbiflat-tembl-idsecond
AP seqret
CL tembl-id:AB000360 test.out -auto
FI test.out
FZ = 2685
FP 1 /^>AB000360 /
FP 1 /^>/
//

ID dbiflat-tembl-last
AP seqret
CL tembl-id:Z69719 test.out -auto
FI test.out
FZ = 34396
FP 1 /^>Z69719 /
FP 1 /^>/
//

ID dbiflat-tembl-nextlast
AP seqret
CL tembl-id:Z52466 test.out -auto
FI test.out
FZ = 500
FP 1 /^>Z52466 /
FP 1 /^>/
//

ID dbiflat-tembl-multiacc
AP seqret
CL tembl-acc:X01958 test.out -auto
FI test.out
FZ = 2225
FP 3 /^>M1190/
FP 3 /^>/
//

ID dbiflat-tembl-all
AP seqret
CL "tembl:*" test.out -auto
FI test.out
FZ = 2847699
FP 3 /^>AF/
FP 3 /^>M1190/
FP 53 /^>/
//

ID dbiflat-tembl-wild
AP seqret
CL "tembl:a*" test.out -auto
FI test.out
FZ = 330041
FP 3 /^>AF/
FP 12 /^>/
//

ID dbiflat-tembl-keyspace
AP seqret
CL "tembl-key:lacy gene" test.out  -osformat embl -auto
FI test.out
FZ = 27194
FP 2 /^KW   .*; lacY gene;/
FP 2 /^ID   /
//

ID dbiflat-tembl-keywild
AP seqret
CL "tembl-key:a*" test.out -auto
FI test.out
FZ = 90158
FP 1 />U01317 /
FP 7 />/
//

#############################################
# The qapflat database
#############################################

ID dbiflat-swiss-keep
DL keep
AP dbiflat
IN SWNEW
IN
IN ../../swnew
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000trembl\.dat\000/
FI entrynam.idx
FZ = 498
FP s /\A.{300}O42495_TAKRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\001/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42495\001/
FI outfile.dbiflat
FC = 32
FP /# Fields: 2\n/
FP /# Files: 1\n/
FP /# Filenames: \*\.dat\n/
FP /filename: 'trembl\.dat'\n    id: 9\n/
FP /Index acc: maxlen 6 items 9\n/
FP /^Total 1 files 9 entries \(0 duplicates\)\n/
FP 1 /^Index \S+ maxlen \d+ items \d+\n/
FP 1 /^filename: /
//

ID dbiflat-swiss-allsys-keep
DL keep
AP dbiflat
CL -fields "acc,sv,des,key,org"
IN SWNEW
IN
IN ../../swnew
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000trembl\.dat\000/
FI entrynam.idx
FZ = 498
FP s /\A.{300}O42495_TAKRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\001/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42495\001/
FI des.trg
FZ = 1286
FP s /\A.{308}1\000/
FI des.hit
FZ = 460
FP s /\A.{300}\004/
FI keyword.trg
FZ = 1164
FP s /\A.{308}COMPLETE PROTEOME\000/
FI keyword.hit
FZ = 432
FP s /\A.{300}\002/
FI seqvn.trg
FZ = 444
FP s /\A.{308}O42495\.0\001/
FI seqvn.hit
FZ = 336
FP s /\A.{300}\001/
FI taxon.trg
FP s /\A.{308}ACANTHOMORPHA\000/
FZ = 867
FI taxon.hit
FZ = 1056
FP s /\A.{300}\001/
FI outfile.dbiflat
FC = 45
FP /# Fields: 6\n/
FP /#   Field 6: org\n/
FP /# Files: 1\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Index sv: maxlen 8 items 9\n/
FP /Index des: maxlen 21 items 34\n/
FP /Index key: maxlen 28 items 24\n/
FP /Index org: maxlen 19 items 21\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
FP 5 /^Index \S+ maxlen \d+ items \d+\n/
FP 1 /^filename: /
//

ID dbiflat-swiss-allnosys-keep
DL keep
AP dbiflat
CL -nosystemsort -fields "acc,sv,des,key,org"
IN SWNEW
IN
IN ../../swnew
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 322
FP s /\A.{300}\001\000trembl\.dat\000/
FI entrynam.idx
FZ = 498
FP s /\A.{300}O42495_TAKRU\000/
FI acnum.hit
FZ = 336
FP s /\A.{300}\001/
FI acnum.trg
FZ = 426
FP s /\A.{308}O42495\001/
FI des.trg
FZ = 1286
FP s /\A.{308}1\000/
FI des.hit
FZ = 460
FP s /\A.{300}\004/
FI keyword.trg
FZ = 1164
FP s /\A.{308}COMPLETE PROTEOME\000/
FI keyword.hit
FZ = 432
FP s /\A.{300}\002/
FI seqvn.trg
FZ = 444
FP s /\A.{308}O42495\.0\001/
FI seqvn.hit
FZ = 336
FP s /\A.{300}\001/
FI taxon.trg
FP s /\A.{308}ACANTHOMORPHA\000/
FZ = 867
FI taxon.hit
FZ = 1056
FP s /\A.{300}\001/
FI outfile.dbiflat
FC = 46
FP /# Fields: 6\n/
FP /#   Field 6: org\n/
FP /# Files: 1\n/
FP /Index acc: maxlen 6 items 9\n/
FP /Index sv: maxlen 8 items 9\n/
FP /Index des: maxlen 21 items 34\n/
FP /Index key: maxlen 28 items 24\n/
FP /Index org: maxlen 19 items 21\n/
FP /Total 1 files 9 entries \(0 duplicates\)\n/
FP 5 /^Index \S+ maxlen \d+ items \d+\n/
FP 1 /^filename: /
//

ID dbiflat-swiss-idfirst
AP seqret
CL qapflat-id:O42495_TAKRU test.out -auto
FI test.out
FZ = 471
FP 1 /^>O42495_TAKRU /
FP 1 /^>/
//

ID dbiflat-swiss-idsecond
AP seqret
CL qapflat-id:Q1KKT3_TAKRU test.out -auto
FI test.out
FZ = 492
FP 1 /^>Q1KKT3_TAKRU /
FP 1 /^>/
//

ID dbiflat-swiss-last
AP seqret
CL qapflat-id:Q68HA9_TAKRU test.out -auto
FI test.out
FZ = 679
FP 1 /^>Q68HA9_TAKRU /
FP 1 /^>/
//

ID dbiflat-swiss-nextlast
AP seqret
CL qapflat-id:Q50J40_TAKRU test.out -auto
FI test.out
FZ = 441
FP 1 /^>Q50J40_TAKRU /
FP 1 /^>/
//

ID dbiflat-swiss-all
AP seqret
CL "qapflat:*" test.out -auto
FI test.out
FZ = 4683
FP 1 /^>Q2KT90_TAKRU /
FP 9 /^>/
//

ID dbiflat-swiss-wild
AP seqret
CL "qapflat:q2*" test.out -auto
FI test.out
FZ = 957
FP 1 /^>Q2KT90_TAKRU /
FP 3 /^>/
//

ID dbiflat-embl-allsys-keep
DL keep
AP dbiflat
CL -fields "acc,sv,des,key,org"
IN EMBL
IN
IN ../../embl
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 586
FP s /\A.{300}\001\000condiv\.dat\000/
FI entrynam.idx
FZ = 1519
FP s /\A.{300}AACY020702065\301/
FI acnum.hit
FZ = 952
FP s /\A.{300}\001/
FI acnum.trg
FZ = 3618
FP s /\A.{308}AACY000000000\003/
FI des.trg
FZ = 7368
FP s /\A.{308}1\000/
FI des.hit
FZ = 2196
FP s /\A.{300}\011/
FI keyword.trg
FZ = 4408
FP s /\A.{308}ACETYLTRANSFERASE\000/
FI keyword.hit
FZ = 676
FP s /\A.{300}\021/
FI seqvn.trg
FZ = 1519
FP s /\A.{308}AACY020702065\.1\001/
FI seqvn.hit
FZ = 512
FP s /\A.{300}\001/
FI taxon.trg
FP s /\A.{308}AFRICAN CLAWED FROG\000/
FZ = 5480
FI taxon.hit
FZ = 3104
FP s /\A.{300}\023/
FI outfile.dbiflat
FC = 141
FP /# Fields: 6\n/
FP /#   Field 6: org\n/
FP /# Files: 13\n/
FP /Index acc: maxlen 13 items 158\n/
FP /Index sv: maxlen 15 items 53\n/
FP /Index des: maxlen 23 items 228\n/
FP /Index key: maxlen 44 items 79\n/
FP /Index org: maxlen 27 items 148\n/
FP /Total 13 files 53 entries \(0 duplicates\)\n/
FP 5 /^Index \S+ maxlen \d+ items \d+\n/
FP 13 /^filename: /
//

ID dbiflat-embl-allnosys-keep
DL keep
AP dbiflat
CL -nosystemsort -fields "acc,sv,des,key,org"
IN EMBL
IN
IN ../../embl
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 586
FP s /\A.{300}\001\000condiv\.dat\000/
FI entrynam.idx
FZ = 1519
FP s /\A.{300}AACY020702065\301/
FI acnum.hit
FZ = 952
FP s /\A.{300}\001/
FI acnum.trg
FZ = 3618
FP s /\A.{308}AACY000000000\003/
FI des.trg
FZ = 7368
FP s /\A.{308}1\000/
FI des.hit
FZ = 2196
FP s /\A.{300}\011/
FI keyword.trg
FZ = 4408
FP s /\A.{308}ACETYLTRANSFERASE\000/
FI keyword.hit
FZ = 676
FP s /\A.{300}\021/
FI seqvn.trg
FZ = 1519
FP s /\A.{308}AACY020702065\.1\001/
FI seqvn.hit
FZ = 512
FP s /\A.{300}\001/
FI taxon.trg
FP s /\A.{308}AFRICAN CLAWED FROG\000/
FZ = 5480
FI taxon.hit
FZ = 3104
FP s /\A.{300}\023/
FI outfile.dbiflat
FC = 142
FP /# Fields: 6\n/
FP /#   Field 6: org\n/
FP /# Files: 13\n/
FP /Index acc: maxlen 13 items 158\n/
FP /Index sv: maxlen 15 items 53\n/
FP /Index des: maxlen 23 items 228\n/
FP /Index key: maxlen 44 items 79\n/
FP /Index org: maxlen 27 items 148\n/
FP /Total 13 files 53 entries \(0 duplicates\)\n/
FP 5 /^Index \S+ maxlen \d+ items \d+\n/
FP 13 /^filename: /
//

ID dbiflat-embl-testexc
AP seqret
CL qanflatexc-id:X13776 test.out -auto
FI test.out
FZ = 2296
FP 1 /^>X13776 /
FP 1 /^>/
//

ID dbiflat-embl-testexcall
AP seqret
CL "qanflatexc-id:*" test.out -auto
FI test.out
FZ = 2842113
FP 1 /^>X13776 /
FP 47 /^>/
//

ID dbiflat-embl-testexcfail
ER 1
AP seqret
CL qanflatexc-id:U68037 test.out -auto
FI stderr
FZ = 124
FP /Error: Unable to read sequence 'qanflatexc-id:U68037'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbiflat-embl-testinc
AP seqret
CL qanflatinc-id:U68037 test.out -auto
FI test.out
FZ = 1318
FP 1 /^>U68037 /
FP 1 /^>/
//

ID dbiflat-embl-testincall
AP seqret
CL "qanflatinc-id:*" test.out -auto
FI test.out
FZ = 5586
FP 1 /^>U68037 /
FP 6 /^>/
//

ID dbiflat-embl-testincfail
ER 1
AP seqret
CL qanflatinc-id:X13776 test.out -auto
FI stderr
FZ = 124
FP /Error: Unable to read sequence 'qanflatinc-id:X13776'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbiflat-genbank-keep
DL keep
AP dbiflat
IN GENBANK
IN GENBANK
IN ../../genbank
IN *.seq
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 520
## Pattern needs 's' modifier ... binary data includes a newline
FP s /\A.{300}\001\000gbbct1\.seq\000/
FI entrynam.idx
FZ = 1041
FP s /\A.{300}AB000095\000/
FI acnum.hit
FZ = 620
FP s /\A.{300}\001/
FI acnum.trg
FZ = 1580
FP s /\A.{308}AB000095\001/
FI outfile.dbiflat
FC = 70
FP /# Fields: 2\n/
FP /# Files: 10\n/
FP /filename: 'gbbct1\.seq'\n    id: 9\n/
FP /filename: 'gbest1\.seq'\n    id: 1\n/
FP /filename: 'gbinv1\.seq'\n    id: 2\n/
FP /filename: 'gbpln1\.seq'\n    id: 1\n/
FP /filename: 'gbpln2\.seq'\n    id: 1\n/
FP /filename: 'gbpri1\.seq'\n    id: 18\n/
FP /filename: 'gbrod1\.seq'\n    id: 3\n/
FP /filename: 'gbsts1\.seq'\n    id: 1\n/
FP /filename: 'gbvrl1\.seq'\n    id: 1\n/
FP /filename: 'gbvrt\.seq'\n    id: 2\n/
FP /Index acc: maxlen 8 items 80\n/
FP /Total 10 files 39 entries \(0 duplicates\)\n/
FP 1 /^Index \S+ maxlen \d+ items \d+\n/
FP 10 /^filename: /
//

#############################################
# The qangcg database(s)
#############################################

ID dbigcg-ex-keep
DL keep
TI 120
AP dbigcg
IN EMBL
IN EMBL
IN ../../embl
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 606
FP s /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/
FI entrynam.idx
FZ = 1020
FP s /\A.{300}AB000095/
FI acnum.hit
FZ = 492
FP s /\A.{300}\001/
FI acnum.trg
FZ = 1068
FP s /\A.{308}AB000095/
FI outfile.dbigcg
FC = 65
FP 9 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 9\n/
FP /#   File \d+: .*\/embl[\/\\]eem_ba1\.seq\n/
FP /Index acc: maxlen 8 items 48\n/
FP /Total 9 files 40 entries \(0 duplicates\)\n/
//

ID dbigcg-id
AP seqret
CL qangcg-id:X65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbigcg-idfirst
AP seqret
CL qangcg-id:AB000095 test.out -auto
FI test.out
FZ = 2542
FP 1 /^>AB000095 /
FP 1 /^>/
//

ID dbigcg-idsecond
AP seqret
CL qangcg-id:AB009062 test.out -auto
FI test.out
FZ = 594
FP 1 /^>AB009062 /
FP 1 /^>/
//

ID dbigcg-last
AP seqret
CL qangcg-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbigcg-nextlast
AP seqret
CL qangcg-id:Z69719 test.out -auto
FI test.out
FZ = 34577
FP 1 /^>Z69719 /
FP 1 /^>/
//

ID dbigcg-acc
AP seqret
CL qangcg:L07770 test.out -auto
FI test.out
FZ = 1775
FP 1 /^>L07770 /
FP 1 /^>/
//

ID dbigcg-splitfirst
AP seqret
CL qangcg-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbigcg-splitmid
AP seqret
CL qangcg-id:AL034557 test.out -auto
FI test.out
FZ = 399267
FP 1 /^>AL034557 /
FP 1 /^>/
//

ID dbigcg-splitbefore
AP seqret
CL qangcg-id:AC017364 test.out -auto
FI test.out
FZ = 3801
FP 1 /^>AC017364 /
FP 1 /^>/
//

ID dbigcg-splitafter
AP seqret
CL qangcg-id:AL035476 test.out -auto
FI test.out
FZ = 326444
FP 1 /^>AL035476 /
FP 1 /^>/
//

ID dbigcg-splitend
AP seqret
CL qangcg-id:U18997 test.out -auto
FI test.out
FZ = 378731
FP 1 /^>U18997 /
FP 1 /^>/
//

ID dbigcg-all
AP seqret
CL "qangcg:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>L07770 /
FP 40 /^>/
//

ID dbigcg-wild
AP seqret
CL "qangcg:a*" test.out -auto
FI test.out
FZ = 1251303
FP 3 /^>AB/
FP 9 /^>A/
FP 9 /^>/
//

ID dbigcg-testexc
AP seqret
CL qangcgexc-id:x65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbigcg-testexcall
AP seqret
CL "qangcgexc-id:*" test.out -auto
FI test.out
FZ = 1744803
FP 1 /^>X65923 /
FP 30 /^>/
//

ID dbigcg-testexcfail
ER 1
AP seqret
CL qangcgexc-id:j01636 test.out -auto
FI stderr
FZ = 123
FP /Error: Unable to read sequence 'qangcgexc-id:j01636'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbigcg-testinc
AP seqret
CL qangcginc-id:j01636 test.out -auto
FI test.out
FZ = 7677
FP 1 /\A>J01636 /
FP 1 /^>/
//

ID dbigcg-testincall
AP seqret
CL "qangcginc-id:*" test.out -auto
FI test.out
FZ = 400271
FP 1 /^>J01636 /
FP 10 /^>/
//

ID dbigcg-testincfail
ER 1
AP seqret
CL qangcginc-id:x65923 test.out -auto
FI stderr
FZ = 123
FP /Error: Unable to read sequence 'qangcginc-id:x65923'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

#############################################
# The qangcgall database(s)
#############################################

ID dbigcg-allsys-keep
DL keep
TI 120
AP dbigcg
CL -fields "acc,sv,des,key,org"
IN EMBL
IN EMBL
IN ../../embl
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning:/
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 606
FP s /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/
FI entrynam.idx
FZ = 1020
FP s /\A.{300}AB000095/
FI acnum.hit
FZ = 492
FP s /\A.{300}\001/
FI acnum.trg
FZ = 1068
FP s /\A.{308}AB000095/
FI des.hit
FZ = 1824
FP s /\A.{300}\023/
FI des.trg
FZ = 5754
FP s /\A.{308}0\000/
FI keyword.hit
FZ = 588
FP s /\A.{300}\047/
FI keyword.trg
FZ = 3264
FP s /\A.{308}16P13\000/
FI seqvn.hit
FZ = 396
FP s /\A.{300}\001/
FI seqvn.trg
FZ = 732
FP s /\A.{308}AB000095\.1/
FI taxon.hit
FZ = 2036
FP s /\A.{300}\016/
FI taxon.trg
FZ = 3765
FP s /\A.{308}AFRICAN CLAWED FROG\000/
FI outfile.dbigcg
FC = 110
FP 9 /^filename: /
FP /# Fields: 6\n/
FP /# Files: 9\n/
FP /#   File \d+: .*\/embl[\/\\]eem_ba1\.seq\n/
FP /Index acc: maxlen 8 items 48\n/
FP /Index sv: maxlen 10 items 24\n/
FP /Index des: maxlen 19 items 202\n/
FP /Index key: maxlen 44 items 57\n/
FP /Index org: maxlen 27 items 99\n/
FP /Total 9 files 40 entries \(0 duplicates\)\n/
//

ID dbigcg-allsys-id
AP seqret
CL qangcgall-id:x65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbigcg-allsys-idfirst
AP seqret
CL qangcgall-id:AB000095 test.out -auto
FI test.out
FZ = 2542
FP 1 /^>AB000095 /
FP 1 /^>/
//

ID dbigcg-allsys-idsecond
AP seqret
CL qangcgall-id:AB009062 test.out -auto
FI test.out
FZ = 594
FP 1 /^>AB009062 /
FP 1 /^>/
//

ID dbigcg-allsys-last
AP seqret
CL qangcgall-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbigcg-allsys-nextlast
AP seqret
CL qangcgall-id:Z69719 test.out -auto
FI test.out
FZ = 34577
FP 1 /^>Z69719 /
FP 1 /^>/
//

ID dbigcg-allsys-acc
AP seqret
CL qangcgall:L07770 test.out -auto
FI test.out
FZ = 1775
FP 1 /^>L07770 /
FP 1 /^>/
//

ID dbigcg-allsys-splitfirst
AP seqret
CL qangcgall-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbigcg-allsys-splitmid
AP seqret
CL qangcgall-id:AL034557 test.out -auto
FI test.out
FZ = 399267
FP 1 /^>AL034557 /
FP 1 /^>/
//

ID dbigcg-allsys-splitbefore
AP seqret
CL qangcgall-id:AC017364 test.out -auto
FI test.out
FZ = 3801
FP 1 /^>AC017364 /
FP 1 /^>/
//

ID dbigcg-allsys-splitafter
AP seqret
CL qangcgall-id:AL035476 test.out -auto
FI test.out
FZ = 326444
FP 1 /^>AL035476 /
FP 1 /^>/
//

ID dbigcg-allsys-splitend
AP seqret
CL qangcgall-id:U18997 test.out -auto
FI test.out
FZ = 378731
FP 1 /^>U18997 /
FP 1 /^>/
//

ID dbigcg-allsys-all
AP seqret
CL "qangcgall:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbigcg-allsys-wild
AP seqret
CL "qangcgall:a*" test.out -auto
FI test.out
FZ = 1251303
FP 9 /^>A/
FP 3 /^>AB/
FP 9 /^>/
//

ID dbigcg-allsys-acnum
AP seqret
CL qangcgall-acc:X65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbigcg-allsys-acnumall
AP seqret
CL "qangcgall-acc:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbigcg-allsys-acnumwild
AP seqret
CL "qangcgall-acc:x*" test.out -auto
FI test.out
FZ = 18988
FP 11 /^>[A-Z0-9]+ X/
FP 11 /^>/
//

ID dbigcg-allsys-sv
AP seqret
CL qangcgall-sv:D00596.1 test.out -auto
FI test.out
FZ = 19008
FP 1 /^>D00596 /
FP 1 /^>/
//

ID dbigcg-allsys-svall
AP seqret
CL "qangcgall-sv:*" test.out -auto
FI test.out
FZ = 2066925
FP 0 /^>X65923 /
FP 1 /^>D00596 /
FP 24 /^>/
//

ID dbigcg-allsys-svwild
AP seqret
CL "qangcgall-sv:x*" test.out -auto
FI test.out
FZ = 5043
FP 3 /^>X/
FP 3 /^>/
//

ID dbigcg-allsys-des
AP seqret
CL qangcgall-des:fau test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbigcg-allsys-desall
AP seqret
CL "qangcgall-des:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbigcg-allsys-deswild
AP seqret
CL "qangcgall-des:m*" test.out -auto
FI test.out
FZ = 1543931
FP 18 /^>.* [Mm]/
FP 18 /^>/
//

ID dbigcg-allsys-key
AP seqret
CL qangcgall-key:rhodopsin test.out -auto
FI test.out
FZ = 5086
FP 1 /^>L07770 /
FP 3 /^>/
//

ID dbigcg-allsys-keyall
AP seqret
CL "qangcgall-key:*" test.out -auto
FI test.out
FZ = 1470428
FP 1 /^>L07770 /
FP 35 /^>/
//

ID dbigcg-allsys-keyspace
AP seqret
CL "qangcgall-key:lacy gene" test.out -osformat embl -auto
FI test.out
FZ = 26226
FP 2 /^KW   .*; lacY gene;/
FP 2 /^ID   /
//

ID dbigcg-allsys-org
AP seqret
CL qangcgall-org:Mus test.out -auto
FI test.out
FZ = 475
FP 1 /^>L48662 /
FP 1 /^>/
//

ID dbigcg-allsys-orgall
AP seqret
CL "qangcgall-org:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbigcg-allsys-orgwild
AP seqret
CL "qangcgall-org:s*" test.out -auto
FI test.out
FZ = 45442
FP 1 /^>L48662/
FP 5 /^>/
//

ID dbigcg-allsys-orgwild2
AP seqret
CL "qangcgall-org:mus*" test.out -auto
FI test.out
FZ = 4276
FP 1 /^>L48662/
FP 2 /^>/
//

ID dbigcg-allnosys-keep
DL keep
TI 120
AP dbigcg
CL -fields "acc,sv,des,key,org" -nosystem
IN EMBL
IN EMBL
IN ../../embl
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning:/
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 606
FP s /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/
FI entrynam.idx
FZ = 1020
FP s /\A.{300}AB000095/
FI acnum.hit
FZ = 492
FP s /\A.{300}\001/
FI acnum.trg
FZ = 1068
FP s /\A.{308}AB000095/
FI des.hit
FZ = 1824
FP s /\A.{300}\023/
FI des.trg
FZ = 5754
FP s /\A.{308}0\000/
FI keyword.hit
FZ = 588
FP s /\A.{300}\047/
FI keyword.trg
FZ = 3264
FP s /\A.{308}16P13\000/
FI seqvn.hit
FZ = 396
FP s /\A.{300}\001/
FI seqvn.trg
FZ = 732
FP s /\A.{308}AB000095\.1/
FI taxon.hit
FZ = 2036
FP s /\A.{300}\016/
FI taxon.trg
FZ = 3765
FP s /\A.{308}AFRICAN CLAWED FROG\000/
FI outfile.dbigcg
FC = 111
FP 9 /^filename: /
FP /# Fields: 6\n/
FP /# Files: 9\n/
FP /#   File \d+: .*\/embl[\/\\]eem_ba1\.seq\n/
FP /Index acc: maxlen 8 items 48\n/
FP /Index sv: maxlen 10 items 24\n/
FP /Index des: maxlen 19 items 202\n/
FP /Index key: maxlen 44 items 57\n/
FP /Index org: maxlen 27 items 99\n/
FP /Total 9 files 40 entries \(0 duplicates\)\n/
//


#############################################
# The qapir database(s)
#############################################

ID dbigcg-pir-keep
DL keep
TI 120
AP dbigcg
IN PIR
IN PIR
IN ../../pir
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning:/
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 388
FP s /\A.{300}\001\000pir1\.ref pir1\.seq\000/
FI entrynam.idx
FZ = 1260
FP s /\A.{300}A31558/
FI acnum.hit
FZ = 672
FP s /\A.{300}\033/
FI acnum.trg
FZ = 1392
FP s /\A.{308}A00001/
FI outfile.dbigcg
FC = 45
FP 4 /^filename: /
FP /# Fields: 2\n/
FP /# Files: 4\n/
FP /#   File \d+: .*\/pir[\/\\]pir1\.seq\n/
FP /Index acc: maxlen 6 items 78\n/
FP /Total 4 files 60 entries \(0 duplicates\)\n/
//

ID dbigcg-pir-id
AP seqret
CL qapir-id:cchu test.out -auto
FI test.out
FZ = 153
FP 1 /\A>CCHU /
FP 1 /^>/
//

ID dbigcg-pir-idfirst
AP seqret
CL qapir-id:A31558 test.out -auto
FI test.out
FZ = 156
FP 1 /^>A31558 /
FP 1 /^>/
//

ID dbigcg-pir-idsecond
AP seqret
CL qapir-id:A32902 test.out -auto
FI test.out
FZ = 123
FP 1 /^>A32902 /
FP 1 /^>/
//

ID dbigcg-pir-last
AP seqret
CL qapir-id:S29350 test.out -auto
FI test.out
FZ = 186
FP 1 /^>S29350 /
FP 1 /^>/
//

ID dbigcg-pir-nextlast
AP seqret
CL qapir-id:S11172 test.out -auto
FI test.out
FZ = 178
FP 1 /^>S11172 /
FP 1 /^>/
//

ID dbigcg-pir-acc
AP seqret
CL qapir:A00001 test.out -auto
FI test.out
FZ = 153
FP 1 /^>CCHU /
FP 1 /^>/
//

ID dbigcg-pir-all
AP seqret
CL "qapir:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>S11172 /
FP 60 /^>/
//

ID dbigcg-pir-wild
AP seqret
CL "qapir:c*" test.out -auto
FI test.out
FZ = 7969
FP 49 /^>C/
FP 49 /^>/
//

ID dbigcg-pir-testexc
AP seqret
CL qapirexc-id:S11172 test.out -auto
FI test.out
FZ = 178
FP 1 /\A>S11172 /
FP 1 /^>/
//

ID dbigcg-pir-testexcall
AP seqret
CL "qapirexc-id:*" test.out -auto
FI test.out
FZ = 2498
FP 1 /^>S11172 /
FP 11 /^>/
//

ID dbigcg-pir-testexcfail
ER 1
AP seqret
CL qapirexc-id:cchu test.out -auto
FI stderr
FZ = 120
FP /Error: Unable to read sequence 'qapirexc-id:cchu'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbigcg-pir-testinc
AP seqret
CL qapirinc-id:cchu test.out -auto
FI test.out
FZ = 153
FP 1 /\A>CCHU /
FP 1 /^>/
//

ID dbigcg-pir-testincall
AP seqret
CL "qapirinc-id:*" test.out -auto
FI test.out
FZ = 7969
FP 1 /^>CCHU /
FP 49 /^>/
//

ID dbigcg-pir-testincfail
ER 1
AP seqret
CL qapirinc-id:S11172 test.out -auto
FI stderr
FZ = 122
FP /Error: Unable to read sequence 'qapirinc-id:S11172'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//


#############################################
# The qapirall database(s)
#############################################

# field sv not supported by PIR format data
ID dbigcg-pirall-keep
DL keep
TI 120
AP dbigcg
CL -fields "acc,des,key,org"
IN PIR
IN PIR
IN ../../pir
IN
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI division.lkp
FZ = 388
FP s /\A.{300}\001\000pir1\.ref pir1\.seq\000/
FI entrynam.idx
FZ = 1260
FP s /\A.{300}A31558/
FI acnum.hit
FZ = 672
FP s /\A.{300}\033/
FI acnum.trg
FZ = 1392
FP s /\A.{308}A00001/
FI des.hit
FZ = 1576
FP s /\A.{300}\066/
FI des.trg
FZ = 3292
FP s /\A.{308}0/
FI keyword.hit
FZ = 2196
FP s /\A.{300}\005/
FI keyword.trg
FZ = 828
FP s /\A.{308}ACETYLATED AMINO END/
FI taxon.hit
FZ = 768
FP s /\A.{300}\$/
FI taxon.trg
FZ = 4944
FP s /\A.{308}AILANTHUS SILKMOTH/
FP /\000ANAS PLATYRHYNCHOS\000/
FP /\000DOMESTIC DUCK\000/
FI outfile.dbigcg
FC = 64
FP 4 /^filename: /
FP /# Fields: 5\n/
FP /# Files: 4\n/
FP /#   File \d+: .*\/pir[\/\\]pir1\.seq\n/
FP /Index acc: maxlen 6 items 78\n/
FP /Index des: maxlen 14 items 136\n/
FP /Index key: maxlen 25 items 16\n/
FP /Index org: maxlen 35 items 108\n/
FP /Total 4 files 60 entries \(0 duplicates\)\n/
//

ID dbigcg-pirall-id
AP seqret
CL qapirall-id:cchu test.out -auto
FI test.out
FZ = 153
FP 1 /\A>CCHU /
FP 1 /^>/
//

ID dbigcg-pirall-idfirst
AP seqret
CL qapirall-id:A31558 test.out -auto
FI test.out
FZ = 156
FP 1 /^>A31558 /
FP 1 /^>/
//

ID dbigcg-pirall-idsecond
AP seqret
CL qapirall-id:A32902 test.out -auto
FI test.out
FZ = 123
FP 1 /^>A32902 /
FP 1 /^>/
//

ID dbigcg-pirall-last
AP seqret
CL qapirall-id:S29350 test.out -auto
FI test.out
FZ = 186
FP 1 /^>S29350 /
FP 1 /^>/
//

ID dbigcg-pirall-nextlast
AP seqret
CL qapirall-id:S11172 test.out -auto
FI test.out
FZ = 178
FP 1 /^>S11172 /
FP 1 /^>/
//

ID dbigcg-pirall-acc
AP seqret
CL qapirall:A00001 test.out -auto
FI test.out
FZ = 153
FP 1 /^>CCHU /
FP 1 /^>/
//

ID dbigcg-pirall-all
AP seqret
CL "qapirall:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>S11172 /
FP 60 /^>/
//

ID dbigcg-pirall-wild
AP seqret
CL "qapirall:c*" test.out -auto
FI test.out
FZ = 7969
FP 49 /^>C/
FP 49 /^>/
//

ID dbigcg-pirall-acnum
AP seqret
CL qapirall-acc:A04605 test.out -auto
FI test.out
FZ = 151
FP 1 /\A>CCRT /
FP 1 /^>/
//

ID dbigcg-pirall-acnumall
AP seqret
CL "qapirall-acc:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>CCRT /
FP 60 /^>/
//

ID dbigcg-pirall-acnumwild
AP seqret
CL "qapirall-acc:s*" test.out -auto
FI test.out
FZ = 841
## CCHO has an S* secondary accession number, rest are primary
FP 4 /^>[A-Z0-9]+ S/
FP 5 /^>/
//

ID dbigcg-pirall-des
AP seqret
CL qapirall-des:cytochrome test.out -auto
FI test.out
FZ = 8825
FP 1 />CCHU /
FP 54 /^>/
//

ID dbigcg-pirall-desall
AP seqret
CL "qapirall-des:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>CCHU /
FP 60 /^>/
//

ID dbigcg-pirall-deswild
AP seqret
CL "qapirall-des:p*" test.out -auto
FI test.out
FZ = 2399
FP 11 /^>.*[ -][Pp]/
FP 11 /^>/
//

ID dbigcg-pirall-key
AP seqret
CL qapirall-key:polymorphism test.out -auto
FI test.out
FZ = 153
FP 1 /^>CCHU /
FP 1 /^>/
//

ID dbigcg-pirall-keyall
AP seqret
CL "qapirall-key:*" test.out -auto
FI test.out
FZ = 9109
FP 1 /^>CCHU /
FP 56 /^>/
//

# only entries with keywords
ID dbigcg-pirall-keyall2
AP seqret
CL "qapirall-key:?*" test.out -auto
FI test.out
FZ = 9109
FP 1 /^>CCHU /
FP 56 /^>/
//

ID dbigcg-pirall-keyspace
AP entret
CL "qapirall-key:blocked amino end" test.out -auto
FI test.out
FZ = 11846
FP 1 /^>P1;CCRT/
FP 8 /^>/
FP 8 /^C;Keywords:.*blocked amino end;/
//

ID dbigcg-pirall-keywild
AP seqret
CL "qapirall-key:m*" test.out -auto
FI test.out
FZ = 8825
FP 1 /^>CCHU /
FP 54 /^>/
//

ID dbigcg-pirall-org
AP seqret
CL "qapirall-org:drosophila melanogaster" test.out -auto
FI test.out
FZ = 180
FP 1 /^>CCFFDM /
FP 1 /^>/
//

ID dbigcg-pirall-orgall
AP seqret
CL "qapirall-org:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>CCHU /
FP 60 /^>/
//

ID dbigcg-pirall-orgwild
AP seqret
CL "qapirall-org:s*" test.out -auto
FI test.out
FZ = 2010
FP 1 /^>CCPG /
FP 12 /^>/
//


ID dbigcg-pirall-orgwild2
AP seqret
CL "qapirall-org:mus*" test.out -auto
FI test.out
FZ = 324
FP 1 /^>CCMS /
FP 2 /^>/
//


#############################################
# The qanxfasta database
#############################################

ID dbxfasta-ex-keep
DL keep
AP dbxfasta
IN emrod
IN emblresource
IN idacc
IN ../../data
IN emrod
IN
IN
IN
FI stderr
FC = 13
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxfasta
FC = 6
FP /Processing file: emrod\nentries: 6 \(6\) /
FP 1 /Processing file: /
FP 1 /^Entry idlen \d+ OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI emrod.ent
FC = 5
FP 1 /^# Number of files: 1\n/
FP /^emrod\n/
FI emrod.pxac
FZ = 284
FP 1 /^Count        6\n/
FP 1 /^Fullcount    6\n/
FI emrod.pxid
FZ = 284
FP 1 /^Count        6\n/
FP 1 /^Fullcount    6\n/
FI emrod.xac
FZ = 2143
FP 1 /z46957/
FP 1 /u68037/
FI emrod.xid
FZ = 2143
FP 1 /z46957/
FP 1 /u68037/
//

ID dbxfasta-allsys-keep
DL keep
AP dbxfasta
CL -fields "id,acc,sv,des"
IN emrod
IN emblresource
IN idsv
IN ../../data
IN emrod
IN
IN
IN
FI stderr
FC = 9
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxfasta
FC = 8
FP /Processing file: emrod\nentries: 6 \(6\) /
FP 1 /Processing file: /
FP 1 /^Entry idlen \d+ OK/
FP 3 /^Field \S+ \S+ \d+ OK/
FP 3 /^Field \S+ /
FI emrod.ent
FC = 5
FP 1 /^# Number of files: 1\n/
FP /^emrod\n/
FI emrod.pxac
FZ = 284
FP 1 /^Count        6\n/
FP 1 /^Fullcount    6\n/
FI emrod.pxde
FZ = 287
FP 1 /^Count        37\n/
FP 1 /^Fullcount    58\n/
FI emrod.pxid
FZ = 284
FP 1 /^Count        6\n/
FP 1 /^Fullcount    6\n/
FI emrod.pxsv
FZ = 284
FP 1 /^Count        6\n/
FP 1 /^Fullcount    6\n/
FI emrod.xac
FZ = 2143
FP 1 /z46957/
FP 1 /u68037/
FI emrod.xde
FZ = 4146
FP 1 /\000antibody\000/
FP 2 /\000chain\000/
FI emrod.xid
FZ = 2143
FP 1 /z46957/
FP 1 /u68037/
FI emrod.xsv
FZ = 2145
FP 1 /z46957\.1/
FP 1 /u68037\.1/
//

ID dbxfasta-idfirst
AP seqret
CL qanxfasta-id:L48662 test.out -auto
FI test.out
FZ = 475
FP 1 /^>L48662 /
FP 1 /^>/
//

ID dbxfasta-idsecond
AP seqret
CL qanxfasta-id:M11903 test.out -auto
FI test.out
FZ = 861
FP 1 /^>M11903 /
FP 1 /^>/
//

ID dbxfasta-last
AP seqret
CL qanxfasta-id:Z46957 test.out -auto
FI test.out
FZ = 1568
FP 1 /^>Z46957 /
FP 1 /^>/
//

ID dbxfasta-nextlast
AP seqret
CL qanxfasta-id:U68037 test.out -auto
FI test.out
FZ = 1318
FP 1 /^>U68037 /
FP 1 /^>/
//

ID dbxfasta-all
AP seqret
CL "qanxfasta:*" test.out -auto
FI test.out
FZ = 5586
FP 1 /^>U68037 /
FP 3 /^>M1190/
FP 6 /^>/
//

ID dbxfasta-wild
AP seqret
CL "qanxfasta:m*" test.out -auto
FI test.out
FZ = 2225
FP 1 /^>M11904 /
FP 3 /^>M/
FP 3 /^>/
//

#############################################
# The qapfasta database
#############################################

ID dbxfasta-swiss-keep
DL keep
AP dbxfasta
IN swnew
IN swissresource
IN idacc
IN ../../data
IN swnew
IN
IN
IN
FI stderr
FC = 13
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxfasta
FC = 6
FP /Processing file: swnew\nentries: 9 \(9\) /
FP 1 /Processing file: /
FP 1 /^Entry idlen \d+ OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI swnew.ent
FC = 5
FP 1 /^# Number of files: 1\n/
FP /^swnew\n/
FI swnew.pxac
FZ = 285
FP 1 /^Count        9\n/
FP 1 /^Fullcount    9\n/
FI swnew.pxid
FZ = 285
FP 1 /^Count        9\n/
FP 1 /^Fullcount    9\n/
FI swnew.xac
FZ = 2143
FP 2 /\000o42495\000/
FP 1 /\000q1kkt3\000/
FI swnew.xid
FZ = 2149
FP 1 /\000q1kkt3_fugru\000/
//

ID dbxfasta-swiss-idfirst
AP seqret
CL qapxfasta-id:O42495_FUGRU test.out -auto
FI test.out
FZ = 470
FP 1 /^>O42495_FUGRU /
FP 1 /^>/
//

ID dbxfasta-swiss-idsecond
AP seqret
CL qapxfasta-id:Q1KKT3_FUGRU test.out -auto
FI test.out
FZ = 465
FP 1 /^>Q1KKT3_FUGRU /
FP 1 /^>/
//

ID dbxfasta-swiss-last
AP seqret
CL qapxfasta-id:Q68HA9_FUGRU test.out -auto
FI test.out
FZ = 678
FP 1 /^>Q68HA9_FUGRU /
FP 1 /^>/
//

ID dbxfasta-swiss-nextlast
AP seqret
CL qapxfasta-id:Q50J40_FUGRU test.out -auto
FI test.out
FZ = 440
FP 1 /^>Q50J40_FUGRU /
FP 1 /^>/
//

ID dbxfasta-swiss-all
AP seqret
CL "qapxfasta:*" test.out -auto
FI test.out
FZ = 4654
FP 1 /^>Q2KT90_FUGRU /
FP 9 /^>/
//

ID dbxfasta-swiss-wild
AP seqret
CL "qapxfasta:q2*" test.out -auto
FI test.out
FZ = 960
FP 1 /^>Q2KT90_FUGRU /
FP 3 /^>Q2/
FP 3 /^>/
//

#############################################
# The qawfasta database
#############################################

ID dbxfasta-worm-keep
DL keep
AP dbxfasta
IN worm
IN dbxresource
IN simple
IN ../../data
IN wormpep.clone.*
IN
IN
IN
FI stderr
FC = 13
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxfasta
FC = 8
FP 2 /Processing file: /
FP 2 /Processing file: wormpep\.clone\./
FP 1 /Processing file: wormpep\.clone\.ZK637\nentries: 66 \(15\) /
FP 1 /^Entry idlen \d+ OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI worm.ent
FC = 6
FP 1 /# Number of files: 2\n/
FP 1 /^wormpep\.clone\.AB\n/
FP 1 /^wormpep\.clone\.ZK637\n/
FI worm.pxac
FZ = 286
FP 1 /^Count        66\n/
FP 1 /^Fullcount    66\n/
FI worm.pxid
FZ = 286
FP 1 /^Count        66\n/
FP 1 /^Fullcount    66\n/
FI worm.xid
FZ = 3794
FP 1 /\000ah10\.1\000/
FI worm.xac
FZ = 3794
FP 1 /\000ah10\.1\000/
//

ID dbxfasta-worm-idfirst
AP seqret
CL qawxfasta-id:AC3.1 test.out -auto
FI test.out
FZ = 426
FP 1 /^>AC3\.1 /
FP 1 /^>/
//

ID dbxfasta-worm-idsecond
AP seqret
CL qawxfasta-id:AC3.2 test.out -auto
FI test.out
FZ = 1057
FP 1 /^>AC3\.2 /
FP 1 /^>/
//

ID dbxfasta-worm-last
AP seqret
CL qawxfasta-id:ZK637.15 test.out -auto
FI test.out
FZ = 205
FP 1 /^>ZK637\.15 /
FP 1 /^>/
//

ID dbxfasta-worm-nextlast
AP seqret
CL qawxfasta-id:zk637.14 test.out -auto
FI test.out
FZ = 260
FP 1 /^>ZK637\.14 /
FP 1 /^>/
//

ID dbxfasta-worm-all
AP seqret
CL "qawxfasta:*" test.out -auto
FI test.out
FZ = 33816
FP 66 /^>/
//

ID dbxfasta-worm-wild
AP seqret
CL "qawxfasta:a*" test.out -auto
FI test.out
FZ = 19764
FP 40 /^>A[^\n]+\n[^>]/
FP 40 /^>/
//

ID dbxfasta-worm-wildz
AP seqret
CL "qawxfasta:z*" test.out -auto
FI test.out
FZ = 7264
FP 15 /^>Z[^\n]+\n[^>]/
FP 15 /^>/
//

#############################################
# The qanxflat database
#############################################

ID dbxflat-ex-keep
DL keep
AP dbxflat
IN embl
IN emblresource
IN embl
IN rod.dat
IN ../../embl
IN
IN
IN
FI stderr
FC = 14
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxflat
FC = 6
FP /^Processing file: rod\.dat\nentries: 6 \(6\)/
FP 1 /^Processing file: /
FP 1 /^Entry idlen 15 OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI embl.ent
FC = 5
FP /^# Number of files: 1\n/
FP /^rod\.dat\n/
FI embl.pxac
FZ = 284
FP /^Count        7\n/
FP /^Fullcount    9\n/
FI embl.pxid
FZ = 284
FP /^Count        6\n/
FP /^Fullcount    6\n/
FI embl.xac
FZ = 2440
FP /\000l48662\000/
FP /\000l48662\000/
FP /\000z46957\000/
FP /\000u68037\000/
FI embl.xid
FZ = 2143
FP /\000l48662\000/
FP /\000z46957\000/
FP /\000u68037\000/
//

ID dbxflat-id
AP seqret
CL qanxflat-id:M11905 test.out -auto
FI test.out
FZ = 654
FP /\A>M11905 /
FP 1 /^>/
//

ID dbxflat-idfirst
AP seqret
CL qanxflat-id:L48662 test.out -auto
FI test.out
FZ = 475
FP 1 /^>L48662 /
FP 1 /^>/
//

ID dbxflat-idsecond
AP seqret
CL qanxflat-id:M11903 test.out -auto
FI test.out
FZ = 861
FP 1 /^>M11903 /
FP 1 /^>/
//

ID dbxflat-last
AP seqret
CL qanflat-id:Z46957 test.out -auto
FI test.out
FZ = 1568
FP 1 /^>Z46957 /
FP 1 /^>/
//

ID dbxflat-nextlast
AP seqret
CL qanxflat-id:U68037 test.out -auto
FI test.out
FZ = 1318
FP 1 /^>U68037 /
FP 1 /^>/
//

ID dbxflat-all
AP seqret
CC Fails to fetch all entries in emboss access method
CL "qanxflat:*" test.out -auto
FI test.out
FZ = 5586
FP 1 /^>L48662 /
FP 6 /^>/
//

ID dbxflat-wild
AP seqret
CL "qanxflat:*7" test.out -auto
FI test.out
FZ = 2886
FP 1 /^>Z46957 /
FP 2 /^>/
//

ID dbxflat-wild2
AP seqret
CL "qanxflat:m119*" test.out -auto
FI test.out
FZ = 2225
FP 1 /^>M11904 /
FP 3 /^>/
//

#############################################
# The qanxflatall database
#############################################

ID dbxflat-all-keep
DL keep
AP dbxflat
CL -fields "id,acc,sv,des,key,org"
IN embl
IN emblresource
IN embl
IN 
IN ../../embl
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxflat
FC = 34
FP /^Processing file: .*rod\.dat\nentries: 44 \(6\)/
FP 13 /^Processing file: /
FP 1 /^Entry idlen 15 OK/
FP 5 /^Field \S+ \S+ \d+ OK/
FP 5 /^Field \S+ /
FI embl.ent
FC = 17
FP /^# Number of files: 13\n/
FP /^rod\.dat\n/
FP 13 /^[a-z0-9]+\.dat\n/
FI embl.pxac
FZ = 288
FP 1 /^Count        158\n/
FP 1 /^Fullcount    163\n/
FI embl.pxde
FZ = 291
FP 1 /^Count        223\n/
FP 1 /^Fullcount    445\n/
FI embl.pxid
FZ = 286
FP 1 /^Count        53\n/
FP 1 /^Fullcount    53\n/
FI embl.pxkw
FZ = 287
FP 1 /^Count        79\n/
FP 1 /^Fullcount    94\n/
FI embl.pxsv
FZ = 286
FP 1 /^Count        53\n/
FP 1 /^Fullcount    53\n/
FI embl.pxtx
FZ = 291
FP 1 /^Count        148\n/
FP 1 /^Fullcount    701\n/
FI embl.xac
FZ = 7084
FP /\000l48662\000/
FP /\000z46957\000/
FP /\000u68037\000/
FI embl.xde
FZ = 15973
FP 2 /\000lactose\000/
FI embl.xid
FZ = 2559
FP /\000l48662\000/
FP /\000z46957\000/
FP /\000u68037\000/
FI embl.xkw
FZ = 6843
FP 2 /\000leghemoglobin\000/
FI embl.xsv
FZ = 2589
FP /\000h45989\.1\000/
FI embl.xtx
FZ = 17498
FP 2 /\000octopoda\000/
//

ID dbxflatall-id
AP seqret
CL qanxflatall-id:L07770 test.out -auto
FI test.out
FZ = 1775
FP /\A>L07770 /
FP 1 />/
//

ID dbxflatall-idfirst
AP seqret
CL qanxflatall-id:AB000095 test.out -auto
FI test.out
FZ = 2542
FP 1 />AB000095 /
FP 1 />/
//

ID dbxflatall-idsecond
AP seqret
CL qanxflatall-id:AB000360 test.out -auto
FI test.out
FZ = 2685
FP 1 />AB000360 /
FP 1 />/
//

ID dbxflatall-last
AP seqret
CL qanxflatall-id:Z69719 test.out -auto
FI test.out
FZ = 34396
FP 1 />Z69719 /
FP 1 />/
//

ID dbxflatall-nextlast
AP seqret
CL qanxflatall-id:Z52466 test.out -auto
FI test.out
FZ = 500
FP 1 />Z52466 /
FP 1 />/
//

ID dbxflatall-all
AP seqret
CC Fails to fetch all entries in emboss access method
CL "qanxflatall:*" test.out -auto
FI test.out
FZ = 2847699
FP 1 />X13776 /
FP 53 />/
//

ID dbxflatall-wild
AP seqret
CL "qanxflatall:a*" test.out -auto
FI test.out
FZ = 330041
FP 3 />AF/
FP 12 />A/
FP 12 />/
//

ID dbxflatall-multiacc
AP seqret
CL qanxflatall-acc:X01958 test.out -auto
FI test.out
FZ = 2225
FP 3 /^>M1190/
FP 3 /^>/
//

ID dbxflatall-keyspace
AP seqret
CL "qanxflatall-key:lacy gene" test.out -osf embl -auto
FI test.out
FZ = 27194
FP 2 /^KW   .*; lacY gene;/
FP 2 /^ID   /
//

ID dbxflatall-keywild
AP seqret
CL "qanxflatall-key:a*" test.out -auto
FI test.out
FZ = 90158
FP 1 />U01317 /
FP 7 />/
//

ID dbxflat-embl-testexc
AP seqret
CL qanxflatexc-id:X13776 test.out -auto
FI test.out
FZ = 2296
FP 1 /^>X13776 /
FP 1 /^>/
//

ID dbxflat-embl-testexcall
AP seqret
CL "qanxflatexc-id:*" test.out -auto
FI test.out
FZ = 2842113
FP 1 /^>X13776 /
FP 47 /^>/
//

ID dbxflat-embl-testexcfail
ER 1
AP seqret
CL qanxflatexc-id:U68037 test.out -auto
FI stderr
FZ = 125
FP /Error: Unable to read sequence 'qanxflatexc-id:U68037'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbxflat-embl-testinc
AP seqret
CL qanxflatinc-id:U68037 test.out -auto
FI test.out
FZ = 1318
FP 1 /^>U68037 /
FP 1 /^>/
//

ID dbxflat-embl-testincall
AP seqret
CL "qanxflatinc-id:*" test.out -auto
FI test.out
FZ = 5586
FP 1 /^>U68037 /
FP 6 /^>/
//

ID dbxflat-embl-testincfail
ER 1
AP seqret
CL qanxflatinc-id:X13776 test.out -auto
FI stderr
FZ = 125
FP /Error: Unable to read sequence 'qanxflatinc-id:X13776'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

#############################################
# The qapxflat database
#############################################

ID dbxflat-swiss-keep
DL keep
AP dbxflat
IN swnew
IN swissresource
IN
IN
IN ../../swnew
IN
IN
IN
IN
FI stderr
FC = 14
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxflat
FC = 6
FP /^Processing file: .*trembl\.dat\nentries: 9 \(9\)/
FP 1 /^Processing file: \S+\.dat/
FP 1 /^Entry idlen 12 OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI swnew.ent
FC = 5
FP /# Number of files: 1\n/
FP /[a-z_]+\.dat\n/
FI swnew.xid
FZ = 2149
FP /\000o42495_takru\000/
FI swnew.xac
FZ = 2143
FP /\000o42495\000/
FI swnew.pxac
FZ = 285
FP 1 /^Count        9\n/
FP 1 /^Fullcount    9\n/
FI swnew.pxid
FZ = 285
FP 1 /^Count        9\n/
FP 1 /^Fullcount    9\n/
//
ID dbxflat-swiss-idfirst
AP seqret
CL qapxflat-id:O42495_TAKRU test.out -auto
FI test.out
FZ = 471
FP 1 /^>O42495_TAKRU /
FP 1 /^>/
//

ID dbxflat-swiss-idsecond
AP seqret
CL qapxflat-id:Q1KKT3_TAKRU test.out -auto
FI test.out
FZ = 492
FP 1 /^>Q1KKT3_TAKRU /
FP 1 /^>/
//

ID dbxflat-swiss-last
AP seqret
CL qapxflat-id:Q68HA9_TAKRU test.out -auto
FI test.out
FZ = 679
FP 1 /^>Q68HA9_TAKRU /
FP 1 /^>/
//

ID dbxflat-swiss-nextlast
AP seqret
CL qapxflat-id:Q50J40_TAKRU test.out -auto
FI test.out
FZ = 441
FP 1 /^>Q50J40_TAKRU /
FP 1 /^>/
//

ID dbxflat-swiss-all
AP seqret
CC Fails to fetch all entries in emboss access method
CL "qapxflat:*" test.out -auto
FI test.out
FZ = 4683
FP 1 /^>Q2KT90_TAKRU /
FP 9 /^>/
//

ID dbxflat-swiss-wild
AP seqret
CL "qapxflat:q2*" test.out -auto
FI test.out
FZ = 957
FP 1 /^>Q2KT90_TAKRU /
FP 3 /^>/
//



#############################################
# The qanxgcg database(s)
#############################################

ID dbxgcg-ex-keep
DL keep
TI 120
AP dbxgcg
IN embl
IN emblresource
IN embl
IN ../../embl
IN
IN
IN
IN
FI stderr
FC = 12
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxgcg
FC = 22
FP 9 /^Processing file: /
FP 9 /^Processing file: eem_[a-z1-9]+\.seq\n/
FP 1 /^Processing file: eem_hum1\.seq\nentries: 32 \(15\) /
FP 1 /^Entry idlen \d+ OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI embl.ent
FC = 13
FP 1 /^Reference 2 filename database\n/
FP 1 /^# Number of files: 9\n/
FP 9 / eem_[a-z1-9]+\.ref\n/
FI embl.pxac
FZ = 286
FP 1 /^Count        48\n/
FP 1 /^Fullcount    48\n/
FI embl.pxid
FZ = 286
FP 1 /^Count        40\n/
FP 1 /^Fullcount    40\n/
FI embl.xac
FZ = 2546
FP 1 /\000ab000095\000/
FI embl.xid
FZ = 2546
FP 1 /\000x65923\000/
//

ID dbxgcg-id
AP seqret
CL qanxgcg-id:X65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbxgcg-idfirst
AP seqret
CL qanxgcg-id:AB000095 test.out -auto
FI test.out
FZ = 2542
FP 1 /^>AB000095 /
FP 1 /^>/
//

ID dbxgcg-idsecond
AP seqret
CL qanxgcg-id:AB009062 test.out -auto
FI test.out
FZ = 594
FP 1 /^>AB009062 /
FP 1 /^>/
//

ID dbxgcg-last
AP seqret
CL qanxgcg-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbxgcg-nextlast
AP seqret
CL qanxgcg-id:Z69719 test.out -auto
FI test.out
FZ = 34577
FP 1 /^>Z69719 /
FP 1 /^>/
//

ID dbxgcg-acc
AP seqret
CL qanxgcg:L07770 test.out -auto
FI test.out
FZ = 1775
FP 1 /^>L07770 /
FP 1 /^>/
//

ID dbxgcg-splitfirst
AP seqret
CL qanxgcg-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbxgcg-splitmid
AP seqret
CL qanxgcg-id:AL034557 test.out -auto
FI test.out
FZ = 399267
FP 1 /^>AL034557 /
FP 1 /^>/
//

ID dbxgcg-splitbefore
AP seqret
CL qanxgcg-id:AL034557 test.out -auto
FI test.out
FZ = 399267
FP 1 /^>AL034557 /
FP 1 /^>/
//

ID dbxgcg-splitafter
AP seqret
CL qanxgcg-id:AL035476 test.out -auto
FI test.out
FZ = 326444
FP 1 /^>AL035476 /
FP 1 /^>/
//

ID dbxgcg-splitend
AP seqret
CL qanxgcg-id:U18997 test.out -auto
FI test.out
FZ = 378731
FP 1 /^>U18997 /
FP 1 /^>/
//

ID dbxgcg-all
AP seqret
CL "qanxgcg:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>L07770 /
FP 40 /^>/
//

ID dbxgcg-wild
AP seqret
CL "qanxgcg:a*" test.out -auto
FI test.out
FZ = 1251303
FP 3 /^>AB/
FP 9 /^>A/
FP 9 /^>/
//

ID dbxgcg-testexc
AP seqret
CL qanxgcgexc-id:x65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbxgcg-testexcall
AP seqret
CL "qanxgcgexc-id:*" test.out -auto
FI test.out
FZ = 1744803
FP 1 /^>X65923 /
FP 30 /^>/
//

ID dbxgcg-testexcfail
ER 1
AP seqret
CL qanxgcgexc-id:j01636 test.out -auto
FI stderr
FZ = 124
FP /Error: Unable to read sequence 'qanxgcgexc-id:j01636'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbxgcg-testinc
AP seqret
CL qanxgcginc-id:j01636 test.out -auto
FI test.out
FZ = 7677
FP 1 /\A>J01636 /
FP 1 /^>/
//

ID dbxgcg-testincall
AP seqret
CL "qanxgcginc-id:*" test.out -auto
FI test.out
FZ = 400271
FP 1 /^>J01636 /
FP 10 /^>/
//

ID dbxgcg-testincfail
ER 1
AP seqret
CL qanxgcginc-id:x65923 test.out -auto
FI stderr
FZ = 124
FP /Error: Unable to read sequence 'qanxgcginc-id:x65923'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

#############################################
# The qangcgall database(s)
#############################################

ID dbxgcg-allsys-keep
DL keep
TI 120
AP dbxgcg
CL -fields "id,acc,sv,des,key,org"
IN embl
IN emblresource
IN embl
IN ../../embl
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning:/
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxgcg
FC = 26
FP 9 /^Processing file: /
FP 9 /^Processing file: eem_[a-z1-9]+\.seq\n/
FP 1 /^Processing file: eem_hum1\.seq\nentries: 32 \(15\) /
FP 1 /^Entry idlen \d+ OK/
FP 5 /^Field \S+ \S+ \d+ OK/
FP 5 /^Field \S+ /
FI embl.ent
FC = 13
FP 1 /^Reference 2 filename database\n/
FP 1 /^# Number of files: 9\n/
FP 9 / eem_[a-z1-9]+\.ref\n/
FI embl.pxac
FZ = 286
FP 1 /^Count        48\n/
FP 1 /^Fullcount    48\n/
FI embl.pxde
FZ = 291
FP 1 /^Count        202\n/
FP 1 /^Fullcount    381\n/
FI embl.pxid
FZ = 286
FP 1 /^Count        40\n/
FP 1 /^Fullcount    40\n/
FI embl.pxkw
FZ = 287
FP 1 /^Count        57\n/
FP 1 /^Fullcount    72\n/
FI embl.pxsv
FZ = 286
FP 1 /^Count        24\n/
FP 1 /^Fullcount    24\n/
FI embl.pxtx
FZ = 290
FP 1 /^Count        99\n/
FP 1 /^Fullcount    434\n/
FI embl.xac
FZ = 2546
FP 1 /\000ab000095\000/
FI embl.xde
FZ = 14084
FP 1 /\000fau\000/
FI embl.xid
FZ = 2546
FP 1 /\000x65923\000/
FI embl.xkw
FZ = 5558
FP 2 /\000mutagenesis\000/
FI embl.xsv
FZ = 2718
FP 1 /\000ab000095\.1\000/
FI embl.xtx
FZ = 11640
FP 1 /\000mus\000/
//

ID dbxgcg-allsys-id
AP seqret
CL qanxgcgall-id:x65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbxgcg-allsys-idfirst
AP seqret
CL qanxgcgall-id:AB000095 test.out -auto
FI test.out
FZ = 2542
FP 1 /^>AB000095 /
FP 1 /^>/
//

ID dbxgcg-allsys-idsecond
AP seqret
CL qanxgcgall-id:AB009062 test.out -auto
FI test.out
FZ = 594
FP 1 /^>AB009062 /
FP 1 /^>/
//

ID dbxgcg-allsys-last
AP seqret
CL qanxgcgall-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbxgcg-allsys-nextlast
AP seqret
CL qanxgcgall-id:Z69719 test.out -auto
FI test.out
FZ = 34577
FP 1 /^>Z69719 /
FP 1 /^>/
//

ID dbxgcg-allsys-acc
AP seqret
CL qanxgcgall:L07770 test.out -auto
FI test.out
FZ = 1775
FP 1 /^>L07770 /
FP 1 /^>/
//

ID dbxgcg-allsys-splitfirst
AP seqret
CL qanxgcgall-id:Z95399 test.out -auto
FI test.out
FZ = 362910
FP 1 /^>Z95399 /
FP 1 /^>/
//

ID dbxgcg-allsys-splitmid
AP seqret
CL qanxgcgall-id:AL034557 test.out -auto
FI test.out
FZ = 399267
FP 1 /^>AL034557 /
FP 1 /^>/
//

ID dbxgcg-allsys-splitbefore
AP seqret
CL qanxgcgall-id:AC017364 test.out -auto
FI test.out
FZ = 3801
FP 1 /^>AC017364 /
FP 1 /^>/
//

ID dbxgcg-allsys-splitafter
AP seqret
CL qanxgcgall-id:AL035476 test.out -auto
FI test.out
FZ = 326444
FP 1 /^>AL035476 /
FP 1 /^>/
//

ID dbxgcg-allsys-splitend
AP seqret
CL qanxgcgall-id:AL035476 test.out -auto
FI test.out
FZ = 326444
FP 1 /^>AL035476 /
FP 1 /^>/
//

ID dbxgcg-allsys-all
AP seqret
CL "qanxgcgall:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbxgcg-allsys-wild
AP seqret
CL "qanxgcgall:a*" test.out -auto
FI test.out
FZ = 1251303
FP 9 /^>A/
FP 3 /^>AB/
FP 9 /^>/
//

ID dbxgcg-allsys-acnum
AP seqret
CL qanxgcgall-acc:X65923 test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbxgcg-allsys-acnumall
AP seqret
CL "qanxgcgall-acc:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbxgcg-allsys-acnumwild
AP seqret
CL "qanxgcgall-acc:x*" test.out -auto
FI test.out
FZ = 18988
FP 11 /^>[A-Z0-9]+ X/
FP 11 /^>/
//

ID dbxgcg-allsys-sv
AP seqret
CL qanxgcgall-sv:D00596.1 test.out -auto
FI test.out
FZ = 19008
FP 1 /^>D00596 /
FP 1 /^>/
//

ID dbxgcg-allsys-svall
AP seqret
CL "qanxgcgall-sv:*" test.out -auto
FI test.out
FZ = 2066925
FP 1 /^>D00596 /
FP 0 /^>X65923 /
FP 24 /^>/
//

ID dbxgcg-allsys-svwild
AP seqret
CL "qanxgcgall-sv:x*" test.out -auto
FI test.out
FZ = 5043
FP 3 /^>X/
FP 3 /^>/
//

ID dbxgcg-allsys-des
AP seqret
CL qanxgcgall-des:fau test.out -auto
FI test.out
FZ = 561
FP 1 /\A>X65923 /
FP 1 /^>/
//

ID dbxgcg-allsys-desall
AP seqret
CL "qanxgcgall-des:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbxgcg-allsys-deswild
AP seqret
CL "qanxgcgall-des:m*" test.out -auto
FI test.out
FZ = 1543931
FP 18 /^>.* [Mm]/
FP 18 /^>/
//

ID dbxgcg-allsys-key
AP seqret
CL qanxgcgall-key:rhodopsin test.out -auto
FI test.out
FZ = 5086
FP 1 /^>L07770 /
FP 3 /^>/
//

ID dbxgcg-allsys-keyall
AP seqret
CL "qanxgcgall-key:*" test.out -auto
FI test.out
FZ = 1470428
FP 1 /^>L07770 /
FP 35 /^>/
//

ID dbxgcg-allsys-keywild
AP seqret
CL "qanxgcgall-key:m*" test.out -auto
FI test.out
FZ = 9919
FP 1 /^>AB009602/
FP 3 /^>/
//

ID dbxgcg-allsys-keyspace
AP seqret
CL "qanxgcgall-key:lacy gene" test.out -osformat embl -auto
FI test.out
FZ = 26226
FP 2 /^KW   .*; lacY gene;/
FP 2 /^ID   /
//

ID dbxgcg-allsys-org
AP seqret
CL qanxgcgall-org:Mus test.out -auto
FI test.out
FZ = 475
FP 1 /^>L48662 /
FP 1 /^>/
//

ID dbxgcg-allsys-orgall
AP seqret
CL "qanxgcgall-org:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbxgcg-allsys-orgwild
AP seqret
CL "qanxgcgall-org:*" test.out -auto
FI test.out
FZ = 2145074
FP 1 /^>X13776 /
FP 40 /^>/
//

ID dbxgcg-allsys-orgwild2
AP seqret
CL "qanxgcgall-org:mus*" test.out -auto
FI test.out
FZ = 4276
FP 1 /^>L48662/
FP 2 /^>/
//

#############################################
# The qaxpir database(s)
#############################################

ID dbxgcg-pir-keep
DL keep
TI 120
AP dbxgcg
IN pir
IN pirresource
IN pir
IN ../../pir
IN
IN
IN
IN
FI stderr
FC = 12
FP 0 /Warning:/
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxgcg
FC = 12
FP 4 /^Processing file: /
FP 4 /^Processing file: pir[1-9]\.seq\n/
FP 1 /^Processing file: pir3\.seq\nentries: 57 \(3\) /
FP 1 /^Entry idlen \d+ OK/
FP 1 /^Field \S+ \S+ \d+ OK/
FP 1 /^Field \S+ /
FI pir.ent
FC = 8
FP 1 /^# Number of files: 4\n/
FP 1 /^Reference 2 filename database\n/
FP 4 /^pir[1-9]\.seq pir[1-9]\.ref\n/
FI pir.pxac
FZ = 287
FP 1 /^Count        78\n/
FP 1 /^Fullcount    93\n/
FI pir.pxid
FZ = 286
FP 1 /^Count        60\n/
FP 1 /^Fullcount    60\n/
FI pir.xac
FZ = 6029
FP 1 /\000a00011\000/
FP 1 /\000a04607\000/
FI pir.xid
FZ = 3018
FP 1 /\000ccms\000/
FP 2 /\000cchu\000/
//

ID dbxgcg-pir-id
AP seqret
CL qaxpir-id:cchu test.out -auto
FI test.out
FZ = 153
FP 1 /\A>CCHU /
FP 1 /^>/
//

ID dbxgcg-pir-idfirst
AP seqret
CL qaxpir-id:A31558 test.out -auto
FI test.out
FZ = 156
FP 1 /^>A31558 /
FP 1 /^>/
//

ID dbxgcg-pir-idsecond
AP seqret
CL qaxpir-id:A32902 test.out -auto
FI test.out
FZ = 123
FP 1 /^>A32902 /
FP 1 /^>/
//

ID dbxgcg-pir-last
AP seqret
CL qaxpir-id:S29350 test.out -auto
FI test.out
FZ = 186
FP 1 /^>S29350 /
FP 1 /^>/
//

ID dbxgcg-pir-nextlast
AP seqret
CL qaxpir-id:S11172 test.out -auto
FI test.out
FZ = 178
FP 1 /^>S11172 /
FP 1 /^>/
//

ID dbxgcg-pir-acc
AP seqret
CL qaxpir:A00001 test.out -auto
FI test.out
FZ = 153
FP 1 /^>CCHU /
FP 1 /^>/
//

ID dbxgcg-pir-all
AP seqret
CL "qaxpir:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>S11172 /
FP 60 /^>/
//

ID dbxgcg-pir-wild
AP seqret
CL "qaxpir:c*" test.out -auto
FI test.out
FZ = 7969
FP 49 /^>C/
FP 49 /^>/
//

ID dbxgcg-pir-testexc
AP seqret
CL qaxpirexc-id:S11172 test.out -auto
FI test.out
FZ = 178
FP 1 /\A>S11172 /
FP 1 /^>/
//

ID dbxgcg-pir-testexcall
AP seqret
CL "qaxpirexc-id:*" test.out -auto
FI test.out
FZ = 2498
FP 1 /^>S11172 /
FP 11 /^>/
//

ID dbxgcg-pir-testexcfail
ER 1
AP seqret
CL qaxpirexc-id:cchu test.out -auto
FI stderr
FZ = 121
FP /Error: Unable to read sequence 'qaxpirexc-id:cchu'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID dbxgcg-pir-testinc
AP seqret
CL qaxpirinc-id:cchu test.out -auto
FI test.out
FZ = 153
FP 1 /\A>CCHU /
FP 1 /^>/
//

ID dbxgcg-pir-testincall
AP seqret
CL "qaxpirinc-id:*" test.out -auto
FI test.out
FZ = 7969
FP 1 /^>CCHU /
FP 49 /^>/
//

ID dbxgcg-pir-testincfail
ER 1
AP seqret
CL qaxpirinc-id:S11172 test.out -auto
FI stderr
FZ = 123
FP /Error: Unable to read sequence 'qaxpirinc-id:S11172'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//


#############################################
# The qapirall database(s)
#############################################

# fields seqvn not supported by PIR format data
ID dbxgcg-pirall-keep
DL keep
TI 120
AP dbxgcg
CL -fields "id,acc,des,key,org"
IN pir
IN pirresource
IN pir
IN ../../pir
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxgcg
FC = 15
FP 4 /^Processing file: /
FP 4 /^Processing file: pir[1-9]\.seq\n/
FP 1 /^Processing file: pir3\.seq\nentries: 57 \(3\) /
FP 1 /^Entry idlen \d+ OK/
FP 4 /^Field \S+ \S+ \d+ OK/
FP 4 /^Field \S+ /
FI pir.ent
FC = 8
FP 1 /^# Number of files: 4\n/
FP 1 /^Reference 2 filename database\n/
FP 4 /^pir[1-9]\.seq pir[1-9]\.ref\n/
FI pir.pxac
FZ = 287
FP 1 /^Count        78\n/
FP 1 /^Fullcount    93\n/
FI pir.pxde
FZ = 289
FP 1 /^Count        136\n/
FP 1 /^Fullcount    319\n/
FI pir.pxid
FZ = 286
FP 1 /^Count        60\n/
FP 1 /^Fullcount    60\n/
FI pir.pxkw
FZ = 287
FP 1 /^Count        16\n/
FP 1 /^Fullcount    474\n/
FI pir.pxtx
FZ = 289
FP 1 /^Count        108\n/
FP 1 /^Fullcount    117\n/
FI pir.xac
FZ = 6029
FP 1 /\000a00011\000/
FP 1 /\000a04607\000/
FI pir.xde
FZ = 10399
FP 1 /\000fragments\000/
FP 2 /\000fragment/
FI pir.xid
FZ = 3018
FP 1 /\000ccms\000/
FP 2 /\000cchu\000/
FI pir.xkw
FZ = 8101
FP 1 /\000heme\000/
FI pir.xtx
FZ = 8353
FP 2 /\000domestic_horse\000/
FP 1 /\000domestic_duck\000/
FP 1 /\000equus_quagga\000/
//

ID dbxgcg-pirall-id
AP seqret
CL qaxpirall-id:cchu test.out -auto
FI test.out
FZ = 153
FP 1 /\A>CCHU /
FP 1 /^>/
//

ID dbxgcg-pirall-idfirst
AP seqret
CL qaxpirall-id:A31558 test.out -auto
FI test.out
FZ = 156
FP 1 /^>A31558 /
FP 1 /^>/
//

ID dbxgcg-pirall-idsecond
AP seqret
CL qaxpirall-id:A32902 test.out -auto
FI test.out
FZ = 123
FP 1 /^>A32902 /
FP 1 /^>/
//

ID dbxgcg-pirall-last
AP seqret
CL qaxpirall-id:S29350 test.out -auto
FI test.out
FZ = 186
FP 1 /^>S29350 /
FP 1 /^>/
//

ID dbxgcg-pirall-nextlast
AP seqret
CL qaxpirall-id:S11172 test.out -auto
FI test.out
FZ = 178
FP 1 /^>S11172 /
FP 1 /^>/
//

ID dbxgcg-pirall-acc
AP seqret
CL qaxpirall:A00001 test.out -auto
FI test.out
FZ = 153
FP 1 /^>CCHU /
FP 1 /^>/
//

ID dbxgcg-pirall-all
AP seqret
CL "qaxpirall:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>S11172 /
FP 60 /^>/
//

ID dbxgcg-pirall-wild
AP seqret
CL "qaxpirall:c*" test.out -auto
FI test.out
FZ = 7969
FP 49 /^>C/
FP 49 /^>/
//

ID dbxgcg-pirall-acnum
AP seqret
CL qaxpirall-acc:A04605 test.out -auto
FI test.out
FZ = 151
FP 1 /\A>CCRT /
FP 1 /^>/
//

ID dbxgcg-pirall-acnumall
AP seqret
CL "qaxpirall-acc:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>CCHU /
FP 1 /^>CCRT /
FP 60 /^>/
//

ID dbxgcg-pirall-acnumwild
AP seqret
CL "qaxpirall-acc:s*" test.out -auto
FI test.out
FZ = 841
## CCHO has an S* secondary accession number, rest are primary
FP 4 /^>[A-Z0-9]+ S/
FP 5 /^>/
//

ID dbxgcg-pirall-des
AP seqret
CL qaxpirall-des:cytochrome test.out -auto
FI test.out
FZ = 8825
FP 1 /^>CCHU /
FP 54 /^>/
//

ID dbxgcg-pirall-desall
AP seqret
CL "qaxpirall-des:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>CCHU /
FP 60 /^>/
//

ID dbxgcg-pirall-deswild
AP seqret
CL "qaxpirall-des:p*" test.out -auto
FI test.out
FZ = 2399
FP 11 /^>.*[ -][Pp]/
FP 11 /^>/
//

ID dbxgcg-pirall-key
AP seqret
CL qaxpirall-key:polymorphism test.out -auto
FI test.out
FZ = 153
FP 1 /^>CCHU /
FP 1 /^>/
//

ID dbxgcg-pirall-keyall
AP seqret
CL "qaxpirall-key:*" test.out -auto
FI test.out
FZ = 9109
FP 1 /^>CCHU /
FP 56 /^>/
//

# only entries with keywords
ID dbxgcg-pirall-keyall2
AP seqret
CL "qaxpirall-key:?*" test.out -auto
FI test.out
FZ = 9109
FP 1 /^>CCHU /
FP 56 /^>/
//

ID dbxgcg-pirall-keyspace
AP entret
CL "qaxpirall-key:blocked amino end" test.out -auto
FI test.out
FZ = 11846
FP 1 /^>P1;CCRT/
FP 8 /^>/
FP 8 /^C;Keywords:.*blocked amino end;/
//

ID dbxgcg-pirall-keywild
AP seqret
CL "qaxpirall-key:m*" test.out -auto
FI test.out
FZ = 8825
FP 1 /^>CCHU /
FP 54 /^>/
//

ID dbxgcg-pirall-org
AP seqret
CL "qaxpirall-org:drosophila melanogaster" test.out -auto
FI test.out
FZ = 180
FP 1 /^>CCFFDM /
FP 1 /^>/
//

ID dbxgcg-pirall-orgall
AP seqret
CL "qaxpirall-org:*" test.out -auto
FI test.out
FZ = 10467
FP 1 /^>CCHU /
FP 60 /^>/
//

ID dbxgcg-pirall-orgwild
AP seqret
CL "qaxpirall-org:s*" test.out -auto
FI test.out
FZ = 2010
FP 1 /^>CCPG /
FP 12 /^>/
//

ID dbxgcg-pirall-orgwild2
AP seqret
CL "qaxpirall-org:mus*" test.out -auto
FI test.out
FZ = 324
FP 1 /^>CCMS /
FP 2 /^>/
//


ID dbxstat-ex
AP dbxstat
IN edam
IN ns
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edam.dbxstat
FC = 7
FP 5 /^ +\d+ [a-z]+\n/
//

ID dbxedam-keep
AP dbxedam
DL keep
IN
IN
IN
IN ../../data/
IN
IN
IN
IN
FI stderr
FC = 12
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxedam
FC = 14
FP 1 /Processing file: /
FI edam.ent
FC = 5
FP 1 /Single filename database\n/
FP /EDAM.obo\n/
FI edam.pxac
FC = 17
FP /^Count +143\n/
FP /^Fullcount +143\n/
FI edam.pxde
FC = 17
FP /^Count +562\n/
FP /^Fullcount +2167\n/
FI edam.pxhasin
FC = 17
FP /^Count +2\n/
FP /^Fullcount +2\n/
FI edam.pxhasout
FC = 17
FP /^Count +2\n/
FP /^Fullcount +2\n/
FI edam.pxid
FC = 17
FP /^Count +143\n/
FP /^Fullcount +143\n/
FI edam.pxis
FC = 17
FP /^Count +90\n/
FP /^Fullcount +225\n/
FI edam.pxisfmt
FC = 17
FP /^Count +5\n/
FP /^Fullcount +5\n/
FI edam.pxisid
FC = 17
FP /^Count +1\n/
FP /^Fullcount +1\n/
FI edam.pxnm
FC = 17
FP /^Count +323\n/
FP /^Fullcount +725\n/
FI edam.pxns
FC = 17
FP /^Count +5\n/
FP /^Fullcount +143\n/
FI edam.xac
FZ = 10926
FP 2 /operation/
FI edam.xde
FZ = 44234
FP 2 /\000fasta\000/
FI edam.xhasin
FZ = 2216
FP 2 /\0000006\000/
FI edam.xhasout
FZ = 2216
FP 2 /\0000006\000/
FI edam.xid
FZ = 4682
FP 2 /\0001915\000/
FI edam.xis
FZ = 7385
FP 2 /\0002069\000/
FI edam.xisfmt
FZ = 2342
FP 2 /\0000006\000/
FI edam.xisid
FZ = 2174
FP 2 /\0000006\000/
FI edam.xnm
FZ = 20835
FP 2 /\000composition\000/
FI edam.xns
FZ = 3708
FP 2 /operation/
FP 2 /\0001422\000/
//

ID dbxedam-idfirst
AP ontoget
CL tedam:0003 -obsolete
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FP /^id: EDAM_topic:0003\n/
FP 1 /^id: /
FP 0 /^is_a: EDAM/
FP 0 /^relationship: /
FC = 16
//

ID dbxedam-idlast
AP ontoget
CL tedam:3016
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FP /^id: EDAM_format:3016\n/
FP 1 /^id: /
FP 1 /^is_a: EDAM_format:2330/
FP 0 /^relationship: /
FC = 10
//

ID dbxobo-keep
AP dbxobo
DL keep
IN edam
IN
IN oboresource
IN ../../data/
IN EDAM.obo
IN *
IN
IN
FI stderr
FC = 8
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxobo
FC = 10
FP 1 /Processing file: /
FI edam.ent
FC = 5
FP 1 /Single filename database\n/
FP /EDAM.obo\n/
FI edam.pxac
FC = 17
FP /^Count +143\n/
FP /^Fullcount +143\n/
FI edam.pxde
FC = 17
FP /^Count +562\n/
FP /^Fullcount +2167\n/
FI edam.pxid
FC = 17
FP /^Count +143\n/
FP /^Fullcount +143\n/
FI edam.pxis
FC = 17
FP /^Count +90\n/
FP /^Fullcount +225\n/
FI edam.pxnm
FC = 17
FP /^Count +323\n/
FP /^Fullcount +725\n/
FI edam.pxns
FC = 17
FP /^Count +5\n/
FP /^Fullcount +143\n/
FI edam.xac
FZ = 19118
FP 2 /\000operation\000/
FI edam.xde
FZ = 44509
FP 2 /\000bootstrapping\000/
FI edam.xid
FZ = 4682
FP 2 /\0001915\000/
FI edam.xis
FZ = 7385
FP 2 /\0002065\000/
FI edam.xnm
FZ = 34576
FP 2 /\000ontologies\000/
FI edam.xns
FZ = 3708
FP 2 /operation/
FP 2 /\0001422\000/
//

ID dbxobo-idfirst
AP ontoget
CL tobo:0003 -obsolete
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FP /^id: EDAM_topic:0003\n/
FP 1 /^id: /
FP 0 /^is_a: EDAM_/
FP 0 /^relationship: /
FC = 16
//

ID dbxobo-idlast
AP ontoget
CL tobo:3016
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FP /^id: EDAM_format:3016\n/
FP 1 /^id: /
FP 1 /^is_a: EDAM_format:2330/
FP 0 /^relationship: /
FC = 10
//

ID dbxresource-keep
AP dbxresource
DL keep
CL drcat
IN drcat
IN drcatresource
IN ../../data/
IN DRCAT.dat
IN
IN
IN
FI stderr
FC = 20
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP 0 /No '[^']+' index found/
FI drcat.ent
FC = 5
FP 1 /[A-z]*\.dat$/
FI drcat.pxac
FC = 17
FP /^Count +22\n/
FP /^Fullcount +22\n/
FI drcat.pxcat
FC = 17
FP /^Count +21\n/
FP /^Fullcount +74\n/
FI drcat.pxde
FC = 17
FP /^Count +829\n/
FP /^Fullcount +2006\n/
FI drcat.pxedat
FC = 17
FP /^Count +61\n/
FP /^Fullcount +152\n/
FI drcat.pxefmt
FC = 17
FP /^Count +11\n/
FP /^Fullcount +135\n/
FI drcat.pxeid
FC = 17
FP /^Count +106\n/
FP /^Fullcount +201\n/
FI drcat.pxetpc
FC = 17
FP /^Count +67\n/
FP /^Fullcount +192\n/
FI drcat.pxid
FC = 17
FP /^Count +110\n/
FP /^Fullcount +110\n/
FI drcat.pxnm
FC = 17
FP /^Count +335\n/
FP /^Fullcount +659\n/
FI drcat.pxqfmt
FC = 17
FP /^Count +16\n/
FP /^Fullcount +148\n/
FI drcat.pxqin
FC = 17
FP /^Count +126\n/
FP /^Fullcount +206\n/
FI drcat.pxqout
FC = 17
FP /^Count +120\n/
FP /^Fullcount +169\n/
FI drcat.pxqurl
FC = 17
FP /^Count +729\n/
FP /^Fullcount +2147\n/
FI drcat.pxrest
FC = 17
FP /^Count +12\n/
FP /^Fullcount +43\n/
FI drcat.pxrf
FC = 17
FP /^Count +5\n/
FP /^Fullcount +83\n/
FI drcat.pxsoap
FC = 17
FP /^Count +18\n/
FP /^Fullcount +23\n/
FI drcat.pxtaxid
FC = 17
FP /^Count +26\n/
FP /^Fullcount +114\n/
FI drcat.pxurl
FC = 17
FP /^Count +227\n/
FP /^Fullcount +585\n/
FI drcat.xac
FZ = 2275
FP 2 /\000apidb\000/
FI drcat.xcat
FZ = 4205
FP 2 /\0002d_gel_databases\000/
FI drcat.xde
FZ = 61212
FP 2 /\000phosphatases\000/
FI drcat.xedat
FZ = 6452
FP 2 /\0002378\000/
FI drcat.xefmt
FZ = 5069
FP 2 /\0002331\000/
FI drcat.xeid
FZ = 8352
FP 2 /\0002291\000/
FI drcat.xetpc
FZ = 7017
FP 2 /\0000166\000/
FI drcat.xid
FZ = 4414
FP 2 /\000panther\000/
FI drcat.xnm
FZ = 24712
FP 2 /\000automatic\000/
FI drcat.xqfmt
FZ = 5469
FP 2 /\000html\000/
FI drcat.xqin
FZ = 11220
FP 2 /\000cdd_id\000/
FI drcat.xqout
FZ = 12809
FP 2 /\000inhibitor_annotation\000/
FI drcat.xqurl
FZ = 64258
FP 2 /\0007tm\000/
FI drcat.xrest
FZ = 3254
FP 2 /\000http\000/
FI drcat.xrf
FZ = 3879
FP 2 /\000sp_explicit\000/
FI drcat.xsoap
FZ = 2998
FP 2 /\000http\000/
FI drcat.xtaxid
FZ = 5062
FP 2 /\0001\000/
FI drcat.xurl
FZ = 19611
FP 2 /\000cornea\000/
FI outfile.dbxresource
FC = 22
FP 1 /Processing file: /
//

ID dbxtax-keep
AP dbxtax
DL keep
TI 1200
IN
IN
IN ../../data/taxonomy
IN
IN
IN
FI stderr
FC = 9
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.dbxtax
FC = 11
FP 1 /Processing file: /
FI taxon.ent
FC = 5
FP 1 /Reference 2 filename database\n/
FP /nodes.dmp names.dmp\n/
FI taxon.pxac
FC = 17
FP /^Count +1\n/
FP /^Fullcount +1\n/
FI taxon.pxgc
FC = 17
FP /^Count +1\n/
FP /^Fullcount +41\n/
FI taxon.pxid
FC = 17
FP /^Count +41\n/
FP /^Fullcount +41\n/
FI taxon.pxmgc
FC = 17
FP /^Count +3\n/
FP /^Fullcount +39\n/
FI taxon.pxtax
FC = 17
FP /^Count +86\n/
FP /^Fullcount +90\n/
FI taxon.pxrnk
FC = 17
FP /^Count +17\n/
FP /^Fullcount +41\n/
FI taxon.pxup
FC = 17
FP /^Count +33\n/
FP /^Fullcount +41\n/
FI taxon.xac
FZ = 2142
FP 2 /\00040673\000/
FI taxon.xgc
FZ = 2168
FP 1 /\0009605\0009606\000/
FI taxon.xid
FZ = 2138
FP 2 /\0001\000/
FI taxon.xmgc
FZ = 2305
FP 1 /\0009605\0009606\000/
FI taxon.xrnk
FZ = 3162
FP 2 /no_rank/
FI taxon.xtax
FZ = 6177
FP 2 /\000eukaryota\000/
FI taxon.xup
FZ = 3882
FP 2 /\0001\000/
//

ID dbxuncompress-keep
DL keep
AP dbxuncompress
PP cp ../dbxflat-all-keep/*de .
CL embl -indexdir . -field des
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP 0 /No '[^']+' index found/
FI embl.pxde
FC = 17
FP /Compress     No\n/
FI embl.xde
FZ = 158208
FP 2 /\000lactose\000/
FI embl.dbxuncompress
FC = 3
FP /Index 'des' uncompressed\n/
//

ID dbxcompress-ex
AP dbxcompress
PP cp ../dbxuncompress-keep/*de .
CL embl -indexdir . -field des
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FP 0 /No '[^']+' index found/
FI embl.pxde
FC = 17
FP /Compress     Yes\n/
FI embl.xde
FZ = 15973
FP 2 /\000lactose\000/
FI embl.dbxcompress
FC = 3
FP /Index 'des' opened, compressing\n/
//

##################################################################
# end of database access tests
##################################################################

ID dbtell-ex
AP dbtell
CL tsw
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 20
FP /^DBNAME tsw \[\n/
FP 6 /^   field: /
FP 1 /^   field:          "id"\n/
//

ID dbxreport-ex
PP cp ../dbxflat-ex-keep/embl.*ac .
PP cp ../dbxflat-ex-keep/embl.*id .
AP dbxreport
CL -indexdir .
IN embl
IN id,acc
IN
QQ rm embl.xac
QQ rm embl.pxac
QQ rm embl.xid
QQ rm embl.pxid
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: / 0 /No '[^']+' index found/
FI embl.dbxreport
FC = 65
FP 2 /Identifier index '[^']+' index found with \d+ pages/
//

ID degapseq-ex
AP degapseq
CL ../../data/dnagap.fasta nogaps.seq
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI nogaps.seq
FZ = 138
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID descseq-ex
UC Set the name of a sequence to "myclone23" 
AP descseq
CL -seq ../../data/dna.text -out clone23.seq -name "myclone23"
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI clone23.seq
FZ = 113
FP /^>myclone23\n/
//

ID descseq-ex2
UC Set the description of a sequence to "This is my clone number 244" 
AP descseq
CL -seq ../../data/dna.text -out xy24.seq -desc "This is my clone number 244"
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI xy24.seq
FZ = 142
FP /EMBOSS_001 This is my clone number 244\n/
//

ID descseq-ex3
UC Append some text to the description of a sequence
AP descseq
CL -seq ../../data/dna.text -out est4.seq -desc " (submitted)" -append
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI est4.seq
FZ = 127
FP /EMBOSS_001  \(submitted\)\n/
//

ID diffseq-ex
AP diffseq
CL tembl:x65923 tembl:ay411291
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.diffseq
FZ = 1624
FP /^# X65923 overlap starts at 57\n/
FP /^# AY411291 overlap starts at 1\n/
FP /^X65923 284-284 Length: 1\n/
FP /^Sequence: c\nFeature: gene 1-402 gene='FAU' locus_tag='HCM4175'\n/
FP /^# Overlap_end: 458 in X65923\n/
FP /^# Overlap_end: 402 in AY411291\n/
FI AY411291.diffgff
FC = 6
FP /^AY411291\tdiffseq\tsequence_conflict\t228\t228\t1\t[+]\t\.\tID=AY411291\.1;note=SNP in X65923;replace=t/
FI X65923.diffgff
FC = 6
FP /^X65923\tdiffseq\tsequence_conflict\t284\t284\t1\t[+]\t\.\tID=X65923\.1;note=SNP in AY411291;replace=c\n/
//

ID diffseq-fwd-fwd
AP diffseq
CL asis::cccctacggggcaaaaagtttt asis::ccccaggggtaaaaatttt -word 4
CL -sid1 fwda -sid2 fwdb
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI fwda.diffseq
FZ = 1277
FP /^# fwda overlap starts at 1\n/
FP /^# fwdb overlap starts at 1\n/
FP /^fwda 5-7 Length: 3\nSequence: tac\nSequence: a\nfwdb 5-5 Length: 1\n/
FP /^fwda 12-12 Length: 1\nSequence: c\nSequence: t\nfwdb 10-10 Length: 1\n/
FP /^fwda 18-18 Length: 1\nSequence: g\nSequence: \nfwdb 15 Length: 0\n/
FP /^# Overlap_end: 22 in fwda\n/
FP /^# Overlap_end: 19 in fwdb\n/
FI fwda.diffgff
FC = 8
FP /^fwda\tdiffseq\tsequence_conflict\t5\t7\t1\t[+]\t\.\tID=fwda\.1;note=fwdb;replace=a/
FP /^fwda\tdiffseq\tsequence_conflict\t12\t12\t1\t[+]\t\.\tID=fwda\.2;note=SNP in fwdb;replace=t/
FP /^fwda\tdiffseq\tsequence_conflict\t18\t18\t1\t[+]\t\.\tID=fwda\.3;note=Insertion of 1 bases in fwda;replace=/
FI fwdb.diffgff
FC = 7
FP /^fwdb\tdiffseq\tsequence_conflict\t5\t5\t1\t[+]\t\.\tID=fwdb\.1;note=fwda;replace=tac\n/
FP /^fwdb\tdiffseq\tsequence_conflict\t10\t10\t1\t[+]\t\.\tID=fwdb\.2;note=SNP in fwda;replace=c\n/
//

ID diffseq-fwd-rev
AP diffseq
CL asis::cccctacggggcaaaaagtttt asis::aaaatttttacccctgggg -word 4
CL -sid1 fwda -sid2 revb -srev2
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI fwda.diffseq
FZ = 1327
FP /^# fwda overlap starts at 1\n/
FP /^# revb overlap starts at 1\n/
FP /^fwda 5-7 Length: 3\nSequence: tac\nSequence: a\nrevb 15-15 Length: 1 \(Reversed\)\n/
FP /^fwda 12-12 Length: 1\nSequence: c\nSequence: t\nrevb 10-10 Length: 1 \(Reversed\)\n/
FP /^fwda 18-18 Length: 1\nSequence: g\nSequence: \nrevb 4 Length: 0 \(Reversed\)\n/
FP /^# Overlap_end: 22 in fwda\n/
FP /^# Overlap_end: 19 in revb\n/
FI fwda.diffgff
FC = 8
FP /^fwda\tdiffseq\tsequence_conflict\t5\t7\t1\t[+]\t\.\tID=fwda\.1;note=revb;replace=a/
FP /^fwda\tdiffseq\tsequence_conflict\t12\t12\t1\t[+]\t\.\tID=fwda\.2;note=SNP in revb;replace=t/
FP /^fwda\tdiffseq\tsequence_conflict\t18\t18\t1\t[+]\t\.\tID=fwda\.3;note=Insertion of 1 bases in fwda;replace=/
FI revb.diffgff
FC = 7
FP /^revb\tdiffseq\tsequence_conflict\t15\t15\t1\t[-]\t\.\tID=revb\.1;note=fwda;replace=tac\n/
FP /^revb\tdiffseq\tsequence_conflict\t10\t10\t1\t[-]\t\.\tID=revb\.2;note=SNP in fwda;replace=c\n/
//

ID diffseq-rev-fwd
AP diffseq
CL asis::aaaactttttgccccgtagggg asis::ccccaggggtaaaaatttt -word 4
CL -sid1 reva -sid2 fwdb  -srev1
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI reva.diffseq
FZ = 1339
FP /^# reva overlap starts at 1\n/
FP /^# fwdb overlap starts at 1\n/
FP /^reva 16-18 Length: 3 \(Reversed\)\nSequence: tac\nSequence: a\nfwdb 5-5 Length: 1\n/
FP /^reva 11-11 Length: 1 \(Reversed\)\nSequence: c\nSequence: t\nfwdb 10-10 Length: 1\n/
FP /^reva 5-5 Length: 1 \(Reversed\)\nSequence: g\nSequence: \nfwdb 15 Length: 0\n/
FP /^# Overlap_end: 22 in reva\n/
FP /^# Overlap_end: 19 in fwdb\n/
FI reva.diffgff
FC = 8
FP /^reva\tdiffseq\tsequence_conflict\t16\t18\t1\t[-]\t\.\tID=reva\.1;note=fwdb;replace=a/
FP /^reva\tdiffseq\tsequence_conflict\t11\t11\t1\t[-]\t\.\tID=reva\.2;note=SNP in fwdb;replace=t/
FP /^reva\tdiffseq\tsequence_conflict\t5\t5\t1\t[-]\t\.\tID=reva\.3;note=Insertion of 1 bases in reva;replace=/
FI fwdb.diffgff
FC = 7
FP /^fwdb\tdiffseq\tsequence_conflict\t5\t5\t1\t[+]\t\.\tID=fwdb\.1;note=reva;replace=tac\n/
FP /^fwdb\tdiffseq\tsequence_conflict\t10\t10\t1\t[+]\t\.\tID=fwdb\.2;note=SNP in reva;replace=c\n/
//

ID diffseq-rev-rev
AP diffseq
CL asis::aaaactttttgccccgtagggg asis::aaaatttttacccctgggg -word 4
CL -sid1 reva -sid2 revb -srev1 -srev2
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI reva.diffseq
FZ = 1389
FP /^# reva overlap starts at 1\n/
FP /^# revb overlap starts at 1\n/
FP /^reva 16-18 Length: 3 \(Reversed\)\nSequence: tac\nSequence: a\nrevb 15-15 Length: 1 \(Reversed\)\n/
FP /^reva 11-11 Length: 1 \(Reversed\)\nSequence: c\nSequence: t\nrevb 10-10 Length: 1 \(Reversed\)\n/
FP /^reva 5-5 Length: 1 \(Reversed\)\nSequence: g\nSequence: \nrevb 4 Length: 0 \(Reversed\)\n/
FP /^# Overlap_end: 22 in reva\n/
FP /^# Overlap_end: 19 in revb\n/
FI reva.diffgff
FC = 8
FP /^reva\tdiffseq\tsequence_conflict\t16\t18\t1\t[-]\t\.\tID=reva\.1;note=revb;replace=a/
FP /^reva\tdiffseq\tsequence_conflict\t11\t11\t1\t[-]\t\.\tID=reva\.2;note=SNP in revb;replace=t/
FP /^reva\tdiffseq\tsequence_conflict\t5\t5\t1\t[-]\t\.\tID=reva\.3;note=Insertion of 1 bases in reva;replace=/
FI revb.diffgff
FC = 7
FP /^revb\tdiffseq\tsequence_conflict\t15\t15\t1\t[-]\t\.\tID=revb\.1;note=reva;replace=tac\n/
FP /^revb\tdiffseq\tsequence_conflict\t10\t10\t1\t[-]\t\.\tID=revb\.2;note=SNP in reva;replace=c\n/
//

ID distmat-ex
AP distmat
CC Example file missing test/data/pax.align
CC No example in the documentation
CL ../../data/pax.align
IN 2
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax.distmat
FP / Kimura /
FP /^\s+0\.00\s+20\.37\s+PX8A_HUMAN 9\n/
FC = 17
//

ID dotmatcher-ex
AP dotmatcher
CL tsw:hba_human tsw:hbb_human -graph cps
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI dotmatcher.ps
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI stdout
FZ = 22
FP /^Created dotmatcher\.ps\n/
//

ID dotmatcher-data
AP dotmatcher
CL tsw:hba_human tsw:hbb_human -graph data
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /Created dotmatcher1\.dat\n/
FI dotmatcher1.dat
FC = 30
FP /^##Maintitle Dotmatcher: tsw-id:HBA_HUMAN vs tsw-id:HBB_HUMAN\n/
FP /^##Subtitle \(windowsize = 10, threshold = 23.00  \d\d\/\d\d\/[0-9][0-9]\)\n/
FP /^Text2 x1 73\.500000 y1 -11\.025001 colour 0 size 1\.000000 HBA_HUMAN\n/
//

ID dotmatcher-stretchdata
AP dotmatcher
CL tsw:hba_human tsw:hbb_human -stretch -xygraph data
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /Created dotmatcher1\.dat\n/
FI dotmatcher1.dat
FC = 27
FP /^##Title Dotmatcher: tsw-id:HBA_HUMAN vs tsw-id:HBB_HUMAN\n/
FP /^##XminA 1\.000000 XmaxA 147\.000000 YminA 1\.000000 YmaxA 142\.000000\n/
FP /^##Xmin 1\.000000 Xmax 147\.000000 Ymin 1\.000000 Ymax 142\.000000\n/
FP /^##ScaleXmin 1\.000000 ScaleXmax 147\.000000 ScaleYmin 1\.000000 ScaleYmax 142\.000000\n/
FP /^##Maintitle \(windowsize = 10, threshold = 23\.00  [0-9\/]+\)\n/
FP /^Line x1 68\.000000 y1 80\.000000 x2 78\.000000 y2 90\.000000 colour 0\n/
FP /^##GraphObjects\n/
FP /^##Number 0\n/
//

ID dotmatcher-stretch
AP dotmatcher
CL tsw:hba_human tsw:hbb_human -xygraph ps -stretch
IN
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 22
FP /^Created dotmatcher\.ps\n/
FI dotmatcher.ps
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID dotpath-ex
AP dotpath
##
## timeout 60 seconds on original test system
##
TI 400
CL tembl:AF129756 tembl:BA000025 -word 20 -graph cps -overlaps
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created dotpath\.ps\n/
FI dotpath.ps
FZ > 16600
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID dotpath-data
AP dotpath
##
## timeout 60 seconds on original test system
##
TI 400
CL tembl:AF129756 tembl:BA000025 -word 20 -graph data
FI dotpath1.dat
FC = 254
FP /^##Maintitle Dotpath: tembl-id:AF129756 vs tembl-id:BA000025\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^Line x1 1\.000000 y1 193957\.000000 x2 153\.000000 y2 194109\.000000 colour 0\n/
FI stdout
FC = 1
FP /^Created dotpath1\.dat\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dottup-ex
AP dottup
CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -graph cps
FI stdout
FZ = 18
FP /^Created dottup\.ps\n/
FI dottup.ps
FC = 2499
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dottup-data
AP dottup
CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636"
CL -graph data
IN
FI stdout
FC = 1
FP /^Created dottup1\.dat\n/
FI dottup1.dat
FC = 2278
FP /^##Maintitle v00294 vs j01636\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^Line x1 625\.000000 y1 5288\.000000 x2 635\.000000 y2 5298\.000000 colour 0\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dottup-stretchdata
AP dottup
CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636"
CL -stretch -xygraph data
IN
FI stdout
FC = 1
FP /^Created dottup1\.dat\n/
FI dottup1.dat
FC = 2265
FP /^Line x1 195\.000000 y1 5510\.000000 x2 206\.000000 y2 5521\.000000 colour 0\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dottup-stretch
AP dottup
CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -xygraph ps
CL -stretch
IN
FI stdout
FZ = 18
FP /^Created dottup\.ps\n/
FI dottup.ps
FZ > 66990
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dreg-ex
AP dreg
IN tembl:x13776
IN ggtacc
IN
FI x13776.dreg
FC = 31
FP /      1       6       [+] regex:GGTACC ggtacc\n/
FP 1 /^# Reported_sequences: 1\n/
FP 1 /^# Reported_hitcount: 1\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dreg-test-multi
AP dreg
CL -sid test
IN asis::TTTATTTTCTATGGGCCGGTATCTTG
IN TT.{0,22}TT
IN
FI test.dreg
FC = 43
FP /      1      25       \+ regex:TT\.\{0,22\}TT TTTATTTTCTATGGGCCGGTATCTT\n/
FP /      1       6       \+ regex:TT\.\{0,22\}TT TTTATT\n/
FP /      2       6       \+ regex:TT\.\{0,22\}TT TTATT\n/
FP 1 /^# Reported_sequences: 1\n/
FP 1 /^# Reported_hitcount: 12\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dreg-test-fwd
AP dreg
CL -rformat listfile
IN asis::caaggttccaacc
IN aa
IN test.out
FI test.out
FC = 33
FP 2 /^asis::/
FP 1 /^asis::caaggttccaacc\[2\:3\]\n/
FP 1 /^asis::caaggttccaacc\[10\:11\]\n/
FP 1 /^# Reported_sequences: 1\n/
FP 1 /^# Reported_hitcount: 2\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID dreg-test-rev
AP dreg
CL -rformat listfile -srev
IN asis::caaggttccaacc
IN aa
IN test.out
FI test.out
FC = 33
FP 1 /^asis::/
FP 1 /^asis::caaggttccaacc\[6:7\:r\]\n/
FP 1 /^# Reported_sequences: 1\n/
FP 1 /^# Reported_hitcount: 1\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//


ID drfinddata-ex
AP drfinddata
CL virus
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI drfinddata.drcat
FC = 32
FP 2 /^ID      /
FP 2 /^EDAMdat 2307 \| Virus annotation\n/
FP 1 /^EDAMdat 2308 \| Virus annotation \(taxonomy\)\n/
FP 2 /^Taxon   10239 \| Viruses\n/
//

ID drfindformat-ex
AP drfindformat
CL fasta
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI drfindformat.drcat
FC = 209
FP 8 /^ID      /
FP 6 /^EDAMfmt 1929 \| FASTA format\n/
FP 2 /^EDAMfmt 2310 \| FASTA-HTML\n/
FP 8 /^Taxon   /
FP 7 /^Taxon   1 /
//

ID drfindid-ex
AP drfindid
CL "uniprot accession"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI drfindid.drcat
FC = 743
FP 37 /^ID      /
//

ID drfindresource-ex
AP drfindresource
CL pathogens
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI drfindresource.drcat
FC = 232
FP 15 /^ID      \S+\n/
FP 15 /^EDAMtpc 0783 \| Pathogens\n/
//

ID drget-ex
AP drget
CL drcat:uniprot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI uniprot.drcat
FC = 22
FP 1 /^ID      \S+\n/
FP 1 /^IDalt   UniProtKB\n/
FP 1 /^EDAMtpc 0639 \| Protein sequence analysis\n/
//

ID drtext-ex
AP drtext
CL drcat:uniprot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI uniprot.drtext
FC = 21
FP 1 /^ID      \S+\n/
FP 1 /^IDalt   UniProtKB\n/
FP 1 /^EDAMtpc 0639 \| Protein sequence analysis\n/
//

ID edamdef-ex
AP edamdef
CL multiple
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamdef.obo
FP /^id: EDAM_data:1234\n/
FC = 353
FP 27 /^id: /
FP 26 /^def: .*multiple /
FP 1 /^def: .*multiple\)/
FP 1 /^def: Multiple /
//

ID edamdef-ex2
AP edamdef
CL multiple -subclasses
## maybe change this example ... Identifier now has 'multiple' in definition
## so we get all identifiers
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamdef.obo
FC = 7759
FP /^id: EDAM_data:1234\n/
FP 586 /^id: /
FP 26 /^def: .*multiple /
FP 1 /^def: .*multiple\)/
FP 1 /^def: Multiple /
//

ID edamdef-nosub
AP edamdef
CL multiple -nosubclasses
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamdef.obo
FP /^id: EDAM_data:1234\n/
FC = 353
FP 27 /^id: /
FP 26 /^def: .*multiple /
FP 1 /^def: .*multiple\)/
FP 1 /^def: Multiple /
//

ID edamhasinput-ex
AP edamhasinput
CL sequence
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamhasinput.obo
FC = 388
FP /^id: EDAM_operation:2507\n/
FP 26 /^id: /
FP 26 /^namespace: operation/
FP 5 /^relationship: has_input EDAM_data:2044 (\{[^\}]+\} )?\! Sequence/
FP 3 /^relationship: has_input EDAM_data:0863 (\{[^\}]+\} )?\! Sequence alignment/
//

ID edamhasoutput-ex
AP edamhasoutput
CL sequence
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamhasoutput.obo
FC = 626
FP /^id: EDAM_operation:0448\n/
FP 43 /^id: /
FP 43 /^namespace: operation/
FP 1 /^relationship: has_output EDAM_data:0849 (\{[^\}]+\} )?\! Sequence record/
FP 5 /^relationship: has_output EDAM_data:1298 (\{[^\}]+\} )?\! Sequence features \(motifs\)/
FP 1 /^relationship: has_output EDAM_data:0857 (\{[^\}]+\} )?\! Database hits \(sequence\)/
FP 1 /^relationship: has_output EDAM_data:0863 (\{[^\}]+\} )?\! Sequence alignment/
//

ID edamisformat-ex
AP edamisformat
CL sequence
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamisformat.obo
FC = 274
FP /^id: EDAM_format:1921\n/
FP 22 /^id: /
FP 22 /^namespace: format/
FP 2 /^relationship: is_format_of EDAM_data:0863 (\{[^\}]+\} )?\! Sequence alignment\n/
FP 1 /^relationship: is_format_of EDAM_data:0924 (\{[^\}]+\} )?\! Sequence trace\n/
//

ID edamisid-ex
AP edamisid
CL sequence
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamisid.obo
FC = 204
FP /^id: EDAM_data:1096\n/
FP 14 /^id:/
FP 14 /^namespace: identifier/
FP 5 /^relationship: is_identifier_of EDAM_data:0849 (\{[^\}]+\} )?\! Sequence record\n/
//

ID edamname-ex
AP edamname
CL "*sequence_set*"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamname.obo
FP /^id: EDAM_data:1234\n/
FP 5 /^id: /
FP 5 /^name: Sequence set/
FP 1 /^name: .*Sequence set$/
FC = 62
//

ID edamname-ex2
AP edamname
CL "*sequence_set*" -subclasses
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI edamname.obo
FC = 291
FP /^id: EDAM_data:1234\n/
FP 22 /^id: /
FP 5 /^name: Sequence set/
//

ID edialign-ex
AP edialign
IN ../../data/vtest.seq
IN
IN
FI vtest.fasta
FC = 12
FP /ldtapC-LFSDGSPQKAAYVLWDQTILQQDITPLPSHethsaqkgELLAliCglraAKPW\n/
FP /pghqkghsaeargnrmADQAARKAAITETPDTSTLL-----\n/
FP /rpgl-CqVFADATPTGWGLVMGHQRMRGTFSAPLPIHta------ELLAa-Cf---ARSR\n/
FP /SGANIIg-----------------------------------------------------\n/
FP /----------------TDNSGRTSLYADSPSVPSHLpdrvh\n/
FP 3 /^>/
FI vtest.edialign
FC = 76
FP 4 /^HTL2 +/
FP /HTL2 +1   ldtapC-LFS DGSPQKAAYV LWDQTILQQD ITPLPSHeth saqkgELLAl \n/
FP / +0000000999 9999999999 9999999999 9999999000 0000000000 \n/
FP / +0000000000 0077777777 7000000000 0000000000 0000000000 \n/
FP / +0000000000 0000000000 0000000000 0000001111 1111111111 \n/
FP / +1111110000 0 \n/
FP /\n/
FP /\n/
FP /\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID einverted-ex
AP einverted
##
## timeout more than 60 seconds
## or we may need a quicker example
##
TI 500
CL tembl:d00596
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI d00596.fasta
FC = 26
FP 8 /^>/
FP /^>D00596_12246_12296\nctcc.*ccatgcc\n>D00596_13886_13938\nggtatgg.*aggag/
FI d00596.inv
FP /Score 236: 108/130 \( 83%\) matches, 0 gaps/
//

ID embossdata-ex
UC Display the directories searched for EMBOSS data files:
AP embossdata
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /Exists\n/
//

ID embossdata-ex2
UC Display the names of data files in all of the possible data directories:
UC This is run on a small test system and so the results will probably
UC be different when you run this.
AP embossdata
CL -showall
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^DIRECTORY: .*data[\/\\]?\n/
FP /^DIRECTORY: .*data[\/\\]CODONS[\/\\]?\n/
FP /^\s*EBLOSUM62\s*\n/
FP /^\s*Eyeast\.cut\s*\n/
//

ID embossdata-exfile
UC Display the directories which contain a particular EMBOSS data file:
AP embossdata
CL EPAM60
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^File \.[\/\\]EPAM60/
FP /^File \.embossdata[\/\\]EPAM60/
//

ID embossdata-exfetch
UC Make a copy of an EMBOSS data file in the current directory:
AP embossdata
CL -fetch Epepcoil.dat
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^File '.*data[\/\\]Epepcoil\.dat' has been copied successfully\.\n/
FI Epepcoil.dat
FZ = 1445
FP /\A# Input data for PEPCOIL *\n/
//

ID embossupdate-ex
AP embossupdate
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^EMBOSS [1-9]\.\d+\.\d+\.\d+ is the latest version \([1-9]\.\d+\.\d+\.\d+\)\n/
//

ID embossversion-ex
AP embossversion
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^[1-9]\.\d+\.\d+\.\d+\n/
//

ID emowse-ex
AP emowse
IN tsw:*
IN ../../data/test.mowse
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cru4_arath.emowse
FC = 177
FP /^1   UBR5_RAT/
FP /1  : UBR5_RAT\s+1\.212e\+0+5 308026\.9   0\.750/
//

ID emma-ex
RQ clustalw
AP emma
IN ../../data/globins.fasta
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
##
## stdout is written by clustalw, invoked by emma
##
## exact output file contents depend on the clustalw version
## this is for clustalw 1.82, built from
## ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.82.UNIX.tar.gz
## file size 606683 date 'Feb  6  2001'
##
## \r? is to test on cygwin systems using a native windows clustalw
##
FI stdout
FC > 50
FP /^Sequences \(1:2\) Aligned\. Score:  83\r?\n/
FP /^Alignment Score 4164\r?\n/
FP /^GCG-Alignment file created +\S+\s*\Z/
FI hbb_human.aln
FZ = 1262
FP /^--------VHLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST\n/
FI hbb_human.dnd
FZ = 186
FP /^HBB_HUMAN:0\.08080,\nHBB_HORSE:0\.08359\)\n/
//

ID emma-dna
RQ clustalw
AP emma
IN ../../data/tropomyosin.fasta
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
##
## stdout is written by clustalw, invoked by emma
##
## exact output file contents depend on the clustalw version
## this is for clustalw 1.82, built from
## ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.82.UNIX.tar.gz
## file size 606683 date 'Feb  6  2001'
##
## \r? is to test on cygwin systems using a native windows clustalw
##
FI stdout
FC = 124
FP /^Sequences \(1:2\) Aligned\. Score:  59\r?\n/
FP /^Alignment Score 127498\r?\n/
FP /^GCG-Alignment file created +\S+\s*\Z/
FI bf056441.aln
FC = 299
FP /^TTC----TTACAAGAGAAGAGAA--AGACCCAC-----GGAGCTCCAG--AGTTTCTGTT\n/
FI bf056441.dnd
FC = 34
FP /^AF186110:0.00114,\n/
FP /AF362887:0.07397\)\n/
FP 11 /^\(\n/
//

ID entret-ex
AP entret
CL tembl:x65923
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.entret
FZ = 3810
FP /^FT   CDS             57\.\.458\n/
FP /^\/\/\Z/
//

ID seq-textauto-acedb
AP entret
CL -auto ../../data/dna.acedb test.out
FI test.out
FZ = 117
FC = 4
FP /DNA : "ACEDB"\n/
FP /GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT/
//

ID seq-text-acedb
AP entret
CL -auto ../../data/dna.acedb -sf acedb test.out
FI test.out
FZ = 117
FC = 4
FP /DNA : "ACEDB"\n/
FP /GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT/
//

ID seq-textauto-codata
AP entret
CL -auto ../../data/dna.codata test.out
FI test.out
FC = 10
FP /^ENTRY           CODATA *\n/
FP /^     91 G T A C G T A C G T\n/
//

ID seq-text-codata
AP entret
CL -auto ../../data/dna.codata -sf codata test.out
FI test.out
FZ = 423
FC = 10
FP /^ENTRY           CODATA *\n/
FP /^     91 G T A C G T A C G T\n/
//

ID seq-textauto-embl
AP entret
CL -auto ../../data/dna.embl test.out
FI test.out
FZ = 487
FC = 18
FP /^ID   EMBL       standard; DNA; UNC; 100 BP\.\n/
FP /^     acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt +100\n/
//

ID seq-text-experiment
AP entret
CL -auto ../../data/xb63c7.s1.exp -sf experiment test.out
FI test.out
FZ = 2317
FC = 51
FP /^ID   xb63c7\.s1\n/
FP /^     TAATTTTCAA AAG-CCA-G\n/
FP /^SR   440\n/
//

ID seq-textauto-experiment
AP entret
CL -auto ../../data/xb63c7.s1.exp test.out
FI test.out
FZ = 2317
FC = 51
FP /^ID   xb63c7\.s1\n/
FP /^     TAATTTTCAA AAG-CCA-G\n/
FP /^SR   440\n/
//

ID seq-text-embl
AP entret
CL -auto ../../data/dna.embl -sf embl test.out
FI test.out
FZ = 487
FC = 18
FP /^ID   EMBL       standard; DNA; UNC; 100 BP\.\n/
FP /^     acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt +100\n/
//

ID seq-textauto-fasta
AP entret
CL -auto ../../data/dna.fasta test.out
FI test.out
FZ = 143
FC = 4
FP /^>FASTA F10002 FASTA FORMAT DNA SEQUENCE\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-text-fasta
AP entret
CL -auto ../../data/dna.fasta -sf fasta test.out
FI test.out
FZ = 143
FC = 4
FP /^>FASTA F10002 FASTA FORMAT DNA SEQUENCE\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-textauto-gcg
AP entret
CL -auto ../../data/dna.gcg test.out
FI test.out
FZ = 362
FC = 14
FP /^GCG  Length: 100  Type: N  Check: 6856 \.\.\n/
FP /^   1 ACGTAC\<note\<GTAC GTACGTACGT\n/
//

ID seq-text-gcg
AP entret
CL -auto ../../data/dna.gcg -sf gcg test.out
FI test.out
FZ = 362
FC = 14
FP /^GCG  Length: 100  Type: N  Check: 6856 \.\.\n/
FP /^   1 ACGTAC\<note\<GTAC GTACGTACGT\n/
//

ID seq-textauto-gcg8
AP entret
CL -auto ../../data/dna.gcg8 test.out
FI test.out
FZ = 182
FC = 7
FP /^GCG8  Length: 100  Check: 6856 \.\.\n/
FP /^  51 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT\n/
//

ID seq-text-gcg8
AP entret
CL -auto ../../data/dna.gcg8 -sf gcg8 test.out
FI test.out
FZ = 182
FC = 7
FP /^GCG8  Length: 100  Check: 6856 \.\.\n/
FP /^  51 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT\n/
//

ID seq-textauto-genbank
AP entret
CL -auto ../../data/dna.genbank test.out
FI test.out
FZ = 268
FC = 8
FP /^LOCUS       GENBANK\n/
FP /^      61  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT\n/
//

ID seq-text-genbank
AP entret
CL -auto ../../data/dna.genbank -sf genbank test.out
FI test.out
FZ = 268
FC = 8
FP /^LOCUS       GENBANK\n/
FP /^      61  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT\n/
//

ID seq-text-ig
AP entret
CL -auto ../../data/dna.ig -sf ig test.out
FI test.out
FZ = 141
FC = 4
FP /^;IG FORMAT DNA SEQUENCE, 100 bases\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT1\n/
//

ID seq-textauto-ncbi
AP entret
CL -auto ../../data/dna.ncbi test.out
FI test.out
FZ = 145
FC = 4
FP /^>gnl\|N10002\|NCBI NCBI FORMAT DNA SEQUENCE\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-text-ncbi
AP entret
CL -auto ../../data/dna.ncbi -sf ncbi test.out
FI test.out
FZ = 145
FC = 4
FP /^>gnl\|N10002\|NCBI NCBI FORMAT DNA SEQUENCE\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-textauto-nbrf
AP entret
CL -auto ../../data/prot.nbrf test.out
FI test.out
FZ = 132
FC = 6
FP /^>P1;pir\n/
FP /^ ABCDEFGHIK LMNPQRSTVW XYZACGTU\.-\n/
//

ID seq-text-nbrf
AP entret
CL -auto ../../data/prot.nbrf -sf nbrf test.out
FI test.out
FZ = 132
FC = 6
FP /^>P1;pir\n/
FP /^ ABCDEFGHIK LMNPQRSTVW XYZACGTU\.-\n/
//

ID seq-textauto-raw
AP entret
CL -auto ../../data/dna.text test.out
FI test.out
FZ = 102
FC = 2
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-text-raw
AP entret
CL -auto ../../data/dna.text -sf raw test.out
FI test.out
FZ = 102
FC = 2
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-textauto-staden
AP entret
CL -auto ../../data/dna.staden test.out
FI test.out
FZ = 102
FC = 2
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-text-staden
AP entret
CL -auto ../../data/dna.staden -sf staden test.out
FI test.out
FZ = 102
FC = 2
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-textauto-strider
AP entret
CL -auto ../../data/dna.strider test.out
FI test.out
FZ = 168
FC = 6
FP /^; DNA sequence STRIDER, 100 bases\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-text-strider
AP entret
CL -auto ../../data/dna.strider -sf strider test.out
FI test.out
FZ = 168
FC = 6
FP /^; DNA sequence STRIDER, 100 bases\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-textauto-textonly
AP entret
CL -auto ../../data/dna.text test.out
FI test.out
FZ = 102
FC = 2
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-text-textonly
AP entret
CL -auto ../../data/dna.text -sf textonly test.out
FI test.out
FZ = 102
FC = 2
FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/
FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-textauto-abi
AP entret
CC Fails ... ABI reading functions use raw file pointer not the buffer
CL -auto ../../data/abiview.abi test.out
FI test.out
FZ = 0
FI stderr
FP /Warning: Failed to read text from binary ABI file \.\.[\/\\]\.\.[\/\\]data[\/\\]abiview\.abi/
FP 1 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID seq-text-selex
AP entret
CL -auto ../../data/test.selex -sf selex test.out
FI test.out
FZ = 610
FC = 20
FP /^#=ID r17\n/
FP /^lig2  AUGGAUGCGCACC AUCA GGGCGUAUCUAU\n/
//

ID seq-textmultiauto-acedb
AP entret
CL -auto ../../data/dna.m-acedb test.out
FI test.out
FZ = 420
FC = 15
FP /^DNA : "ACEDBM1"\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-textmulti-acedb
AP entret
CL -auto ../../data/dna.m-acedb -sf acedb test.out
FI test.out
FZ = 420
FC = 15
FP /^DNA : "ACEDBM1"\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-textmultiauto-codata
AP entret
CL -auto ../../data/dna.m-codata test.out
FI test.out
FZ = 1416
FC = 30
FP /^ENTRY           CODATAM1 +\n/
FP /^     91 G T A C G T A C G T A C G T A C G T A C G T A C G T A C G T\n/
//

ID seq-textmulti-codata
AP entret
CL -auto ../../data/dna.m-codata -sf codata test.out
FI test.out
FZ = 1416
FC = 30
FP /^ENTRY           CODATAM1 +\n/
FP /^     91 G T A C G T A C G T A C G T A C G T A C G T A C G T A C G T\n/
//

ID seq-textmultiauto-embl
AP entret
CL -auto ../../data/dna.m-embl test.out
FI test.out
FZ = 945
FC = 21
FP 3 /^ID/
FP /^ +CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT +120\n/
//

ID seq-textmulti-embl
AP entret
CL -auto ../../data/dna.m-embl -sf embl test.out
FI test.out
FZ = 945
FC = 21
FP 3 /^ID/
FP /^ +CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT +120\n/
//

ID seq-textmultiauto-fasta
AP entret
CL -auto ../../data/dna.m-fasta test.out
FI test.out
FZ = 516
FC = 12
FP 3 /^>/
FP /^CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA\n/
//

ID seq-textmulti-fasta
AP entret
CL -auto ../../data/dna.m-fasta -sf fasta test.out
FI test.out
FZ = 516
FC = 12
FP 3 /^>/
FP /^CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA\n/
//

ID seq-textmultiauto-msf
AP entret
CL -auto ../../data/dna.msf test.out
FI test.out
FZ = 820
FC = 22
FP 3 /^ Name: MSF/
FP /^        MSFM3  ACGTACGTAC GTACGTACGT\n/
//

ID seq-textmulti-msf
AP entret
CL -auto ../../data/dna.msf -sf msf test.out
FI test.out
FZ = 820
FC = 22
FP 3 /^ Name: MSF/
FP /^        MSFM3  ACGTACGTAC GTACGTACGT\n/
//

ID seq-textmultiauto-msf8
AP entret
CL -auto ../../data/dna.msf8 test.out
FI test.out
FZ = 1084
FC = 30
FP 3 /^ Name: fastam/
FP /^fastam3  TACGTACGTA CGTACGTACG T\n/
//

ID seq-textmulti-msf8
AP entret
CL -auto ../../data/dna.msf8 -sf msf test.out
FI test.out
FZ = 1084
FC = 30
FP 3 /^ Name: fastam/
FP /^fastam3  TACGTACGTA CGTACGTACG T\n/
//

ID seq-textmultiauto-ncbi
AP entret
CL -auto ../../data/dna.m-ncbi test.out
FI test.out
FZ = 594
FC = 12
FP 3 /^>/
FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/
//

ID seq-textmulti-ncbi
AP entret
CL -auto ../../data/dna.m-ncbi -sf ncbi test.out
FI test.out
FZ = 594
FC = 12
FP 3 /^>/
FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/
//

ID seq-textmultiauto-phylip
AP entret
CL -auto ../../data/dna.phylip test.out
FI test.out
FZ = 495
FC = 12
FP 3 /^MSFM/
FP /^          ACGTACGTTG CAACGTACGT\n/
//

ID seq-textmulti-phylip
AP entret
CL -auto ../../data/dna.phylip -sf phylip test.out
FI test.out
FZ = 495
FC = 12
FP 3 /^MSFM/
FP /^          ACGTACGTTG CAACGTACGT\n/
//

ID seq-textmultiauto-phylipnon
AP entret
CL -auto ../../data/dna.phylip3 test.out
FI test.out
FZ = 492
FC = 10
FP 3 /^MSFM/
FP /^          ACGTACGTTG CAACGTACGT\n/
//

ID seq-textmulti-phylipnon
AP entret
CL -auto ../../data/dna.phylip3 -sf phylip test.out
FI test.out
FZ = 492
FC = 10
FP 3 /^MSFM/
FP /^          ACGTACGTTG CAACGTACGT\n/
//

ID seq-textmultiauto-strider
AP entret
CL -auto ../../data/dna.m-strider test.out
FI test.out
FZ = 648
FC = 21
FP 3 /^; DNA sequence  STRIDERM/
FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/
//

ID seq-textmulti-strider
AP entret
CL -auto ../../data/dna.m-strider -sf strider test.out
FI test.out
FZ = 648
FC = 21
FP 3 /^; DNA sequence  STRIDERM/
FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/
//

ID seq-textauto-nonewline
AP entret
CL -auto ../../data/dna.nonewline test.out
FI test.out
FZ = 51
FC = 2
FP /^>\n/
FP /^aaaaccccggggttttaaaaccccggggttttaaccggttshshshsh$/
//

ID seq-textauto-empty
AP entret
CL -auto stdin test.out
ER 1
FI stderr
FZ = 109
FP /Error: Unable to read sequence 'stdin'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID epestfind-ex
AP epestfind
CL -graph cps -invalid
IN ../../data/exu2_drops.sw
IN 
IN 
IN 
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 21
FP /^Created epestfind\.ps\n/
FI exu2_drops.epestfind
FZ = 3194
FP /238 KMVYEMALQLIESESTESPESFESPESSESSEAEVK 273/
FI epestfind.ps
FC = 523
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID eprimer3-ex
RQ primer3
AP eprimer3
CL tembl:x65921 x65921.eprimer3 -explain
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.eprimer3
FZ = 1427
FP /^\n/
FP /^# considered 16422\n/
FP /^# GC content failed 156\n/
FP /^# ok 2960\n/
FP /^# considered 16330\n/
FP /^# ok 2902\n/
FP /^# considered 2652\n/
FP /^# unacceptable product size 2444\n/
FP /^# ok 186\n/
FP /^   1 PRODUCT SIZE: 202\n/
FP /^     FORWARD PRIMER     801   20  59\.72  60\.00  CCCAGGAGCTACACACCTTC\n/
FP /^     REVERSE PRIMER     983   20  59\.81  55\.00  GGAGCACGACTTGATCTTCC\n/
FP 5 /PRODUCT SIZE: +[0-9]+/
//

ID eprimer32-ex
RQ primer32
AP eprimer32
CL tembl:x65921 x65921.eprimer32 -explain
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.eprimer32
FZ = 1321
FP /^\n/
FP /^# considered 18855\n/
FP /^# GC content failed 156\n/
FP /^# ok 5416\n/
FP /^# considered 18706\n/
FP /^# ok 5348\n/
FP /^# considered 3726\n/
FP /^# unacceptable product size 3429\n/
FP /^# ok 297\n/
FP /^     FORWARD PRIMER     981   20  60\.11  55\.00  CCGGAAGATCAAGTCGTGCT\n/
FP /^     REVERSE PRIMER    1162   20  59\.90  55\.00  GGTGTGACACTCAGCTGTCA\n/
FP 5 /^     FORWARD PRIMER\s+\d+/
FP 5 /^     REVERSE PRIMER\s+\d+/
//

ID eprimer32-okregion
RQ primer32
AP eprimer32
CL tembl:x65921 x65921.eprimer32 -explain -okleft '980+20' -okright '1160+19'
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.eprimer32
FZ = 834
FP /^\n/
FP 0 /^# GC content failed /
FP 0 /^# unacceptable product size/
FP 2 /^# considered 19170\n/
FP 2 /^# ok 3\n/
FP /^# ok 1\n/
FP /^# considered 3\n/
FP /^# not in any ok left region 19164\n/
FP /^# not in any ok right region 19167\n/
FP /^     FORWARD PRIMER     980   20  61\.08  60\.00  CCCGGAAGATCAAGTCGTGC\n/
FP /^     REVERSE PRIMER    1160   19  57\.79  57\.90  GTGACACTCAGCTGTCAGG\n/
FP 3 /^     FORWARD PRIMER\s+\d+/
FP 3 /^     REVERSE PRIMER\s+\d+/
//

ID equicktandem-ex
UC The input sequence is the human herpesvirus tandem repeat.
AP equicktandem
CL -noorigfile
IN tembl:L46634
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.qtan
FC = 25
FP /^ +191     935       [+]     339      6    124\n/
//

ID est2genome-ex
TI 200
AP est2genome
IN tembl:h45989
IN tembl:z69719
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI h45989.est2genome
FZ = 3050
FP /Note .* forward est and forward genome, .* imply REVERSED GENE/
FP /^Exon       163  91\.8 25685 25874 Z69719           1   193 H45989/
//

ID est2genome-pax
TI 200
AP est2genome
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2103
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
//

ID est2genome-align
TI 200
AP est2genome
CL -align
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 8086
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
FP /^HSA1280   9567 ttgaggccctggagaaaggtgat\.\.\.\.\.ttcagagtttgagagaacccat  10116\n/
FP /^               [|]+>>>>> 515 >>>>>[|]+\n/
FP /^   pax6   1082 ttgaggccctggagaaag\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.agtttgagagaacccat   1116\n/
//

ID est2genome-align-linear
TI 200
AP est2genome
CL -align -space 2
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 8086
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
FP /^HSA1280   9567 ttgaggccctggagaaaggtgat\.\.\.\.\.ttcagagtttgagagaacccat  10116\n/
FP /^               [|]+>>>>> 515 >>>>>[|]+\n/
FP /^   pax6   1082 ttgaggccctggagaaag\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.agtttgagagaacccat   1116\n/
//

ID est2genome-align-best
TI 200
AP est2genome
CL -align -best
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 8086
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
//

ID est2genome-mode-both
TI 200
AP est2genome
CL -mode both
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2103
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
//

ID est2genome-mode-both2
TI 200
AP est2genome
CL -sreverse -mode both
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2104
FP /Note .* forward est and forward genome, .* imply REVERSED GENE/
FP /^Exon       129  99\.2 20744 20874 HSA1280       1141  1271 pax6/
CC Note the nosplice version of this test does not have "REVERSED GENE"
CC This is only because with no splice consensus penalty the same score
CC is found in both directions and the forward gene is the one reported
//

ID est2genome-mode-forward
TI 200
AP est2genome
CL -mode forward
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2050
FP /Note requested forward est and forward genome/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
//

ID est2genome-mode-reverse
TI 200
AP est2genome
CL -mode reverse -srev1
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2051
FP /Note requested reversed est and forward genome/
FP /^Exon       129  99\.2  1380  1510 HSA1280        428   558 pax6/
//

ID est2genome-mode-reverse2
TI 200
AP est2genome
CL -mode reverse
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 47
FP /Note requested reversed est and forward genome/
FP 0 /^Exon/
//

ID est2genome-nosplice-both
TI 200
AP est2genome
CL -nousesplice -mode both
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2103
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       124  99\.2  1380  1505 HSA1280        428   553 pax6/
//

ID est2genome-nosplice-both2
TI 200
AP est2genome
CL -sreverse -nousesplice -mode both
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2103
FP /Note .* forward est and forward genome, .* imply forward gene/
FP /^Exon       132  99\.3 20741 20874 HSA1280       1138  1271 pax6/
CC Note the mode version of this test has "imply REVERSED GENE"
CC This is only because with no splice consensus penalty the same score
CC is found in both directions and the forward gene is the one reported
//

ID est2genome-nosplice-forward
TI 200
AP est2genome
CL -nousesplice -mode forward
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2050
FP /Note requested forward est and forward genome/
FP /^Exon       124  99\.2  1380  1505 HSA1280        428   553 pax6/
//

ID est2genome-nosplice-reverse
TI 200
AP est2genome
CL -nousesplice -mode reverse -srev1
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 2051
FP /Note requested reversed est and forward genome/
FP /^Exon       124  99\.2  1380  1505 HSA1280        428   553 pax6/
//

ID est2genome-nosplice-reverse2
TI 200
AP est2genome
CL -nousesplice -mode reverse
IN ../../data/pax6_cdna.fasta
IN ../../data/z83307.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pax6.est2genome
FZ = 47
FP /Note requested reversed est and forward genome/
FP 0 /^Exon/
//

ID etandem-ex
UC The input sequence is the human herpesvirus tandem repeat. 
AP etandem
CL -noorigfile
IN tembl:L46634
IN 6
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.tan
FC = 33
FP /^# HitCount: 5\n/
FP /^    793     936       [+]     120      6     24     93\.8 acccta   \n/
FP /^    793     936       [+]     120      6     24     93\.8 acccta   \n/
FP /^    432     485       [+]      38      6      9     90\.7 ccctaa   \n/
FP /^    494     529       [+]      26      6      6     94\.4 ccctaa   \n/
FP /^    568     597       [+]      24      6      5    100\.0 aaccct   \n/
//

ID extractalign-ex
UC Extract the region from position 10 to 20:
AP extractalign
CL ../../data/dna.msf result.seq -regions "11-30"
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI result.seq
FZ = 84
FP /^GTACGTACGT----ACGTAC\n/
FP 3 /^>/
//

ID extractfeat-ex
UC To write out the exons of a sequence: 
AP extractfeat
CL tembl:x65921 -type exon
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.fasta
FZ = 743
FP 5 /^>X65921_/
FP /^>X65921_951_1095 \[exon\] H\.sapiens fau 1 gene\n/
FP /^gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag\n/
//

ID extractfeat-ex2
UC To write out the exons with 10 extra bases at the start and end so that you can inspect the splice sites:
AP extractfeat
CL tembl:x65921 -type exon -before 10 -after 10
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.fasta
FZ = 844
FP 5 /^>X65921_/
FP /^>X65921_951_1095 \[exon\] H\.sapiens fau 1 gene\n/
FP /^cccactacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagact\n/
FP /^cctaaggtgagtgaga\n/
//

ID extractfeat-ex3
UC To write out the 10 bases around the start of all 'exon' features in the tembl database: 
AP extractfeat
CL "tembl:*"  -type exon -before 5 -after -5
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI em498477.fasta
FZ = 85782
FP 5 /^>X65921_/
FP 811 /^>/
FP /^>X65921_951_1095 \[exon\] H\.sapiens fau 1 gene\n/
//

ID extractfeat-ex4
UC To extract the CDS region with the exons joined into one sequence:
AP extractfeat
CL tembl:x65921 -type CDS -join
IN
FI stderr
FC = 2
FI x65921.fasta
FZ = 453
FP /^>X65921_782_1912 \[CDS\] H\.sapiens fau 1 gene\n/
//

# The example has phosphorylation, we only have features that say
# PHOSPHORYLATION (BY RK) (BY SIMILARITY).
ID extractfeat-ex5
UC To write out the 7 residues around all phosphorylated serine residues
## in the tsw database
AP extractfeat
CL "tsw:*" -type MOD_RES -value "phosphoserine*" -before 3 -after -4
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cru4_arath.fasta
FZ = 7500
FP 43 /^>/
FP 43 /\[post_translationally_modified_region\]/
FP /^>OPSD_HUMAN_343_343 \[post_translationally_modified_region] Rhodopsin \(Opsin-2\)\n/
FP /^TETSQVA\n/
FP /^>PAXI_HUMAN_109_109 \[post_translationally_modified_region] Paxillin\n/
FP /^SPCSRVG\n/
//

# use database entry in example
ID extractseq-ex
UC Extract the region from position 10 to 20:
AP extractseq
CL tembl:x65923 result.seq -regions "10-20"
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI result.seq
FZ = 48
FP /^ctcgactccat\n/
//

# use database entry in example
ID extractseq-ex2
UC Extract the regions 10 to 20, 30 to 45, 533 to 537:
AP extractseq
CL tembl:x65921 result2.seq -regions "10-20 30-45 533-537"
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI result2.seq
FZ = 71
FP /^tccctctcgatacactcgggacaagttagggc\n/
//

# use database entry in example
ID extractseq-ex3
UC Extract the regions 782-856, 951-1095, 1557-1612 and 1787-1912:
AP extractseq
CL tembl:x65921 -reg "782..856,951..1095,1557..1612,1787..1912" stdout
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 8
FZ = 447
FP /^atgcagctctttg[^\n]+ccaggaaacg/
FP /^cccacctttggcaagaagaagggccccaatgccaactcttaa\n/
//

ID extractseq-ex4
UC Extract the regions 782-856, 951-1095, 1557-1612 and 1787-1912 all to separate output sequences:
AP extractseq
CL tembl:x65921 -reg "782..856,951..1095,1557..1612,1787..1912" stdout -separate
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 13
FZ = 564
FP /^>X65921_782_856/
FP /atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg\ngtcgcccagatcaag/
FP /gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag/
FP /^tcttaa\n/
//

ID featcopy-ex
AP featcopy
IN ../../data/paamir.gff3
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.gff
FC = 15
FP /X13776\tEMBL\tdatabank_entry\t1\t2167\t\.\t\+\t\.\tID=X13776\.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type=genomic DNA;db_xref=taxon:287\n/
FP /X13776\tEMBL\tsequence_feature\t1\t1\t\.\t\+\t.\tID=X13776.8;note=last base of an XhoI site\n/
//

ID featmerge-ex
AP featmerge
IN tsw:actb1_takru
IN ../antigenic-keep/actb1_takru.antigenic
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI actb1_takru.gff
FC = 30
FP 18 /ACTB1_TAKRU\tantigenic\tepitope\t/
FP 7 /ACTB1_TAKRU\tSWISSPROT/
//

ID feattext-ex
AP feattext
IN ../../data/paamir.gff3
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.feattext
FC = 15
FP /X13776\tEMBL\tdatabank_entry\t1\t2167\t\.\t\+\t\.\tID=X13776\.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type=genomic DNA;db_xref=taxon:287\n/
FP /X13776\tEMBL\tsequence_feature\t1\t1\t\.\t\+\t.\tID=X13776.8;note=last base of an XhoI site\n/
//

ID featreport-ex
AP featreport
IN ../../data/paamir.fasta
IN ../../data/paamir.gff
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 15
FP /\A##gff-version 3\n/
FP 10 /^PAAMIR\tEMBL\t/
//

ID findkm-ex
AP findkm
CL -graph cps
IN ../../data/enztest.dat
IN
FI stdout
FZ = 18
FP /^Created findkm\.ps\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI enztest.findkm
FP /^Vmax = 99\.70, Km = 4\.8946\d+\n/
FI findkm.ps
FC = 547
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID freak-ex
AP freak
CL tembl:x65923
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.freak
FZ = 9828
FP /^24         0\.733333\n/
FP /^36         0\.600000\n/
FP /^489        0\.266667\Z/
//

ID fuzznuc-ex
AP fuzznuc
IN tembl:L46634
IN AAGCTT
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.fuzznuc
FC = 35
FP /^# HitCount: 2\n/
FP /^      1       6       [+] pattern:AAGCTT        . aagctt\n/
FP /^   1267    1272       [+] pattern:AAGCTT        . aagctt\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 2\n/
//

ID fuzznuc-rev
AP fuzznuc
CL -complement
IN asis::GATAAAAAAAAAAAAAAAAAAAAAAAAGATAAAATATCGATA
IN GATA
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 39
FP /^# HitCount: 4\n/
FP /^      1       4       [+] pattern:GATA        . GATA\n/
FP /^     28      31       [+] pattern:GATA        . GATA\n/
FP /^     39      42       [+] pattern:GATA        . GATA\n/
FP /^     35      38       [-] pattern:GATA        . GATA\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 4\n/
//

ID fuzznuc-ex2
AP fuzznuc
IN tembl:L46634
IN @../../data/nucseq.pat
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.fuzznuc
FC = 35
FP /^# HitCount: 2\n/
FP /^    429     448       [+] targetseq:cg\(2\)c\(3\)taaccctagc\(3\)ta        \. cggccctaaccctagcccta\n/
FP /^    491     510       [+] targetseq:cg\(2\)c\(3\)taaccctagc\(3\)ta        \. cggccctaaccctagcccta\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 2\n/
//

ID fuzznuc-ex3
AP fuzznuc
CL -pname test
IN tembl:L46634
IN @../../data/nucsimple.pat
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.fuzznuc
FC = 48
FP /^# HitCount: 13\n/
FP /^    429     438       [+] test1:cg\(2\)c\(3\)taac        \. cggccctaac\n/
FP /^    801     810       [+] test2:cctagc\(3\)ta          \. cctagcccta\n/
FP 8 /^ +\d+ +\d+       [+-] test1:+/
FP 5 /^ +\d+ +\d+       [+-] test2:+/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 13\n/
//

ID fuzznuc-ex4
AP fuzznuc
IN tembl:L46634
IN @../../data/nuc.pat
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.fuzznuc
FC = 62
FP /^# HitCount: 27\n/
FP /^    429     448       [+] pat1:cggccctaaccctagcccta            \. cggccctaaccctagcccta\n/
FP /^    491     510       [+] pat2:cg\(2\)c\(3\)taaccctagc\(3\)ta        \. cggccctaaccctagcccta\n/
FP /^    535     554       [+] pat2:cg\(2\)c\(3\)taaccctagc\(3\)ta        1 cggccctaaccctaacccta\n/
FP /^    753     763       [+] pat3:cggc\(2,4\)taac\(2,5\)              . cggccctaacc\n/
FP /^    753     764       [+] pat3:cggc\(2,4\)taac\(2,5\)              . cggccctaaccc\n/
FP 16 /^\s+\d+\s+\d+\s+[+-]\s+pat3:/
FP 9 /^\s+\d+\s+\d+\s+[+-]\s+pat2:/
FP 7 /^\s+\d+\s+\d+\s+[+-]\s+pat2:\S+\s+1\s+/
FP 2 /^\s+\d+\s+\d+\s+[+-]\s+pat2:\S+\s+\.\s+/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 27\n/
//

ID fuzznuc-mismatch
AP fuzznuc
CL -pattern @../../data/barcodes.pat -pmismatch 1
IN ../../data/barcodes.seq
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI barcodes.fuzznuc
FC = 39
FP /^# HitCount: 3\n/
FP /^      1      14       \+ bc_1:tcaggtagtactcg        1 tcagctagtactcg\n/
FP /^     15      28       \+ bc_2:tcagggctaggcat        1 tcagcgctaggcat\n/
FP /^     29      42       \+ bc_3:cgacctcgactcga        1 cgacgtcgactcga\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 3\n/
//

ID fuzzpro-ex
AP fuzzpro
IN tsw:*
IN [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cru4_arath.fuzzpro
FC = 137
FP 8 /^# HitCount: 1\n/
FP 8 /^# HitCount: [1-9]\d*/
FP /^     53      63 pattern:\[FY\]-\[LIV\]-G-\[DE\]-E-A-Q-x-\[RKQ\]\(2\)-G        . YVGDEAQSKRG\n/
FP 4 /^     53      63 pattern:\[FY\]-\[LIV\]-G-\[DE\]-E-A-Q-x-\[RKQ\]\(2\)-G        . YVGDEAQSKRG\n/
FP 4 /^     55      65 pattern:\[FY\]-\[LIV\]-G-\[DE\]-E-A-Q-x-\[RKQ\]\(2\)-G        . YVGDEAQSKRG\n/
FP /^# Reported_sequences: 8\n/
FP /^# Reported_hitcount: 8\n/
//

ID fuzztran-ex
AP fuzztran
CL -opt
IN tembl:Z46957
IN RA
IN f
IN
IN
FI stderr
FC = 31
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI z46957.fuzztran
FC = 44
FP /^# HitCount: 9\n/
FP /^    919     924       [+]       2 pattern:RA        .      1    307    308 RA         \n/
FP /^    752     757       [+]       2 pattern:RA        .      2    251    252 RA         \n/
FP /^     72      77       [+]       2 pattern:RA        .      3     24     25 RA         \n/
FP 6 /^.* 1 +\d+ +\d+ RA +\n/
FP 2 /^.* 2 +\d+ +\d+ RA +\n/
FP 1 /^.* 3 +\d+ +\d+ RA +\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 9\n/
//

ID seq-infeat-embl
TI 120
AP seqret
CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft embl::test.out -auto
FI test.out
FZ = 78245
## one_of to order
FP /^FT   polyA_signal    order\(368\.\.373,459\.\.464\)\n/
## group to order
FP /^FT   misc_feature    order\(226\.\.288,688\.\.754\)\n/
## Internal quotes
FP /^FT                   ""amiE"" gene"\n/
## Bad features type (CODS) to misc_feature
FP /^FT   misc_feature    135\.\.1292\n/
## Case fix for tag /Translation
FP /^FT                   \/translation="MSANSL/
## Case fix for type Cds
FP /^FT   CDS             1289\.\.1879\n/
## Cleanup of extra white space 'positive  regulator'
FP /\/note="aliphatic amidase regulator, positive regulator of\n/
//

ID seq-outfeat-gff
AP seqret
CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft gff::test.out -auto
FI test.out
FC = 648
FZ = 58255
## Internal quotes
FP /\tCDS\t1289\t1879\t\.\t\+\t0\tID=AB036666\.87;.* of "amiE" /
//

ID seq-outfeat-gb
AP seqret
CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft gb::test.out -auto
FI test.out
FZ = 75593
## Internal quotes
FP /^                     ""amiE"" gene"\n/
## Bad features type (CODS) to misc_feature
FP /^     misc_feature    135\.\.1292\n/
## Case fix for tag /Translation
FP /^                     \/translation="MSANSL/
## Case fix for type Cds
FP /^     CDS             1289\.\.1879\n/
## Cleanup of extra white space 'positive  regulator'
FP /\/note="aliphatic amidase regulator, positive regulator of\n/
//

ID seq-infeat-genbank
AP seqret
CL -feat ../../data/feat.fasta -ufo ../../data/feat.gbft em::test.out -auto
FI test.out
FZ = 78387
## Internal quotes
FP /^FT                   ""amiE"" gene"\n/
## Bad features type (CODS) to misc_feature
FP /^FT   misc_feature    135\.\.1292\n/
## Case fix for tag /Translation
FP /^FT                   \/translation="MSANSL/
## Case fix for type Cds
FP /^FT   CDS             1289\.\.1879\n/
## Cleanup of extra white space 'positive  regulator'
FP /\/note="aliphatic amidase regulator, positive regulator of\n/
//

ID seq-infeat-genbank-toembl
AP seqret
CL -feat ../../data/feat.fasta -ufo ../../data/feat.gbft em::test.out -auto
FI test.out
FZ = 78387
## Internal quotes
FP /^FT                   ""amiE"" gene"\n/
## Bad features type (CODS) to misc_feature
FP /^FT   misc_feature    135\.\.1292\n/
## Case fix for tag /Translation
FP /^FT                   \/translation="MSANSL/
## Case fix for type Cds
FP /^FT   CDS             1289\.\.1879\n/
## Cleanup of extra white space 'positive  regulator'
FP /\/note="aliphatic amidase regulator, positive regulator of\n/
//

ID seq-infeat-genpept-toswiss
AP seqret
CL -feat ../../data/acn78416.genpept -sf genpept test.out -osf swiss -auto
FI test.out
FC = 28
FP 2 /^RN   /
FP /^ID   .* 225 AA\.\n/
FP /^DT   21-MAR-2009, entry version 1.\n/
FP /^SQ   SEQUENCE   225 AA;  25874 MW;  EDD076FAC2CFFD74 CRC64;\n/
//

ID seq-infeat-pir
AP seqret
CL -feat ../../data/featprot.fasta -ufo pir::../../data/feat.pir sw::test.out -auto
FI test.out
FZ = 5120
## active site two locations with copied annotation (note and comment)
FP /^FT   ACT_SITE     38     38       Cys, His \(status experimental\)\.\n/
FP /^FT   ACT_SITE     90     90       Cys, His \(status experimental\)\.\n/
//

ID seq-infeatauto-pir
AP seqret
CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir sw::test.out -auto
FI test.out
FZ = 5120
## active site two locations with copied annotation (note and comment)
FP /^FT   ACT_SITE     38     38       Cys, His \(status experimental\)\.\n/
FP /^FT   ACT_SITE     90     90       Cys, His \(status experimental\)\.\n/
//

ID seq-infeat-nbrf
AP seqret
CL -feat ../../data/featprot.fasta -ufo nbrf::../../data/feat.pir sw::test.out -auto
FI test.out
FZ = 5120
## active site two locations with copied annotation (note and comment)
FP /^FT   ACT_SITE     38     38       Cys, His \(status experimental\)\.\n/
FP /^FT   ACT_SITE     90     90       Cys, His \(status experimental\)\.\n/
//

ID seq-infeat-pir-togff
AP seqret
CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir gff::test.out -auto
FI test.out
FC = 67
FZ = 5645
## active site two locations with copied annotation (note and comment)
FP /^OPSD_HUMAN\tPIR\tbiological_region\t38\t90\t\.\t\.\t\.\tID=OPSD_HUMAN\.24;featflags=type:active_site_residue;note=Cys%2C His;comment=status experimental\n/
FP /^OPSD_HUMAN\tPIR\tactive_site_residue\t90\t90\t\.\t\.\t\.\tParent=OPSD_HUMAN.24\n/
//

ID seq-infeat-pir-topir
AP seqret
CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir pir::test.out -auto
FI test.out
FZ = 1756
## active site two locations with copied annotation (note and comment)
FP /^F;38,90\/Active site: Cys, His #status experimental\n/
//

ID seq-infeat-refseqp
AP seqret
CL -feat ../../data/protein.refseqp  sw::test.out -auto
FI test.out
FZ = 7288
## active site two locations with copied annotation (note and comment)
FP /^FT   SIGNAL        1     21       ifn-beta. 2410.\n/
FP /^FT   SITE         97     97       other. N-glycosylation site. CDD:28979.\n/
//

ID seq-infeat-swiss
AP seqret
CL -feat tsw:laci_ecoli sw::test.out -auto
FI test.out
FZ = 14091
FP /^FT   DNA_BIND      6     25       H-T-H motif\.\n/
FP /^FT   HELIX        74     89\n/
//

ID seq-infeat-swiss-topir
AP seqret
CL -feat tsw:laci_ecoli pir::test.out -auto
FI test.out
FZ = 1923
FP /^F;6-25\/Binding site: H-T-H motif, DNA_contact\n/
FP /^F;74-89\/Region: alpha_helix\n/
//

ID seq-infeat-swiss-togff
AP seqret
CL -feat tsw:laci_ecoli gff::test.out -auto
FI test.out
FC = 55
FZ = 3518
FP /^LACI_ECOLI\tSWISSPROT\tDNA_contact\t6\t25\t\.\t\.\t\.\tID=LACI_ECOLI\.3;note=H-T-H motif\n/
FP /^LACI_ECOLI\tSWISSPROT\talpha_helix\t74\t89\t\.\t\.\t\.\tID=LACI_ECOLI\.14\n/
//

ID garnier-ex
AP garnier
IN tsw:amic_pseae
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amic_pseae.garnier
FC = 84
FP /^#  Residue totals: H:103   E:102   T: 86   C: 94\n/
FP /RADA\nhelix                HHHHHH            HHHH H     HHHHHH\n/
FP 1 /^# Reported_sequences: 1\n/
FP 1 /^# Reported_hitcount: 113\n/
//

ID garnier-range
AP garnier
CL -sbegin 51 -send 120
IN tsw:amic_pseae
IN
FI stderr
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FC = 2
FI amic_pseae.garnier
FC = 50
FP /^#  Residue totals: H: 17   E: 22   T: 21   C: 10\n/
FP /RADA\nhelix                HHHHHH            HHHH H     HHHHHH\n/
FP /^turns        T TTT  TTT   \n/
FP 1 /^# Reported_sequences: 1\n/
FP 1 /^# Reported_hitcount: 25\n/
//

ID garnier-short
AP garnier
IN asis::GSHQERPL
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI asis.garnier
FP /^#  Residue totals: H:  0   E:  0   T:  2   C:  6\n/
FP /^turns       TT\n/
FP /^ coil CCCCCC  \n/
//

ID geecee-ex
AP geecee
CL tembl:L46634
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l46634.geecee
FZ = 42
FP /^L46634        0\.53\n/
//

ID getorf-ex
AP getorf
CL -minsize 300
IN tembl:v00294
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00294.orf
FZ = 876
FP /^>V00294_1 \[735 - 1112\]/
FP /^TGKRAV\n/
FP /^>V00294_2 \[1 - 1110\]/
FP /^RQVSRLESGQ\n/
FP /^>V00294_3 \[465 - 49\]/
//

ID godef-ex
AP godef
CL glycoprotein
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI godef.obo
FP /^id: GO:0015572\n/
FC = 867
FP 76 /^id: /
FP 59 /^def: .*glycoprotein /
FP 12 /^def: .*glycoprotein\./
FP 5 /^def: .*glycoprotein,/
//

ID goname-ex
AP goname
CL glycoprotein
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI goname.obo
FP /^id: GO:0009306\n/
FP /^id: GO:0003980\n/
FC = 1054
FP 62 /^id: /
FP 32 /^def: .*glycoprotein/
FP 39 /^name: .*glycoprotein/
FP 116 /^synonym: .*glycoprotein/
//

ID helixturnhelix-ex
AP helixturnhelix
IN tsw:laci_ecoli
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.hth
FP /^[(]1[)] Score 2160\.000 length 22 at residues 4->25\n/
FP /^ Standard_deviations: 6\.54\n/
//

ID hmoment-ex
AP hmoment
CL tsw:hbb_human
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hbb_human.hmoment
FZ = 1494
FP /^Window: 10 Angle: 100 Max uH: 0\.714\n/
FP /^138\s+0\.299\Z/
//

ID iep-ex
AP iep
CL tsw:laci_ecoli
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.iep
FZ = 761 
FP /^Isoelectric Point = 6\.8385\n/
FP /^  7\.00    43\.37    -0\.63\n/
//

ID iep-ex2
AP iep
CL tsw:ifna2_human -disulphide 2 -lysinemodified 2 
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ifna2_human.iep
FZ = 762 
FP /^Isoelectric Point = 5\.7240\n/
FP /^  7\.00    27\.44    -2\.56\n/
//

ID iep-ifna2-nooptions
AP iep
CL tsw:ifna2_human
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ifna2_human.iep
FZ = 762 
FP /^Isoelectric Point = 6\.6891\n/
FP /^  7\.00    33\.32    -0\.68\n/
//

# change examples to .msf from .seq
#
ID infoalign-ex
AP infoalign
CL ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 8
FP /^msf::\S+msf:HBA_HORSE\s+HBA_HORSE\s+141\s+144\s+2\s+3\s+63\s+6\s+72\s+56\.250000\s+0\.830000\s+\n/
//

ID infoalign-ex2
UC This example doesn't display the USA of the sequence:
AP infoalign
CL ../../data/globins.msf -nousa
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 8
FP /^HBA_HORSE\s+141\s+144\s+2\s+3\s+63\s+6\s+72\s+56\.250000\s+0\.830000\s+\n/
//

ID infoalign-ex3
UC Display only the name and sequence length of a sequence:
AP infoalign
CL ../../data/globins.msf -only -name -seqlength
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 7
FP /^HBA_HORSE\s+141\n/
//

ID infoalign-ex4
UC Display only the name, number of gap characters and differences to the consensus sequence:
AP infoalign
CL ../../data/globins.msf -only -name -gapcount -diffcount
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 7
FP /^HBA_HORSE\s+3\s+72\n/
//

ID infoalign-ex5
UC Display the name and number of gaps within a sequence:
AP infoalign
CL ../../data/globins.msf -only -name -gaps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 7
FP /^HBA_HORSE\s+2\n/
//

ID infoalign-ex6
UC Display information formatted with HTML:
AP infoalign
CL ../../data/globins.msf -html
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 94
FP /^<tr><td>msf::\.\./\.\./data/globins\.msf:HBA_HORSE<\/td>\n/
FP /^<td>HBA_HORSE<\/td>\n/
//

ID infoalign-ex7
UC Use the first sequence as the reference sequence to compare to:
AP infoalign
CL ../../data/globins.msf -refseq 1
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.infoalign
FC = 8
FP /^msf::\S+\s+HBA_HORSE\s+141\s+144\s+2\s+3\s+51\s+18\s+72\s+64\.583336\s+0\.830000\s+\n/
//

ID infoalign-ex8
AP infoalign
CL -auto @../../data/eclac.list -out test.out
FI test.out
FC = 6
FP /tembl-id:J01636\s+J01636\s+7477\s+7477\s+0\s+0\s+374\s+0\s+7103\s+94\.997[0-9]+\s+1\.0+\s+E.*/
FP /tembl-id:V00296\s+V00296\s+3078\s+3078\s+0\s+0\s+373\s+0\s+2705\s+87\.881[0-9]+\s+1\.0+\s+E.*/
//

ID infoalign-ex9
AP infoalign
CL -auto tembl:v00296 -out test.out
FI test.out
FC = 2
FP /tembl-id:V00296\s+V00296\s+3078\s+3078\s+0\s+0\s+3078\s+0\s+0\s+0\.0+\s+1\.0+\s+E.*/
//

ID infobase-ex
AP infobase
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.infobase
FC = 18
FP /A    A          T          adenine\n/
FP /K    GT         M          keto_base\n/
//

ID inforesidue-ex
AP inforesidue
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.inforesidue
FC = 27
FP /A    Ala   alanine                 0.0   71.0788 tiny,small,aliphatic,nonpolar  A\n/
FP /Z    Glx   glutamate/glutamine    -0.5  128.6231 polar                          EQ\n/
//

ID infoseq-ex
UC Display information on a sequence:
AP infoseq
CL tembl:x13776
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 304
FP /^tembl-id:X13776\s+tembl\s+X13776\s+X13776\s+N\s+2167\s+66\.54\s+Pseudomonas/
//

ID infoseq-ex2
UC Don't display the USA of a sequence:
AP infoseq
CL tembl:x13776 -nousa
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 254
FP /^tembl\s+X13776\s+X13776\s+N\s+2167\s+66\.54\s+Pseudomonas/
//

ID infoseq-ex3
UC Display only the name and length of a sequence:
AP infoseq
CL tembl:x13776 -only -name -length
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 46
FP /^X13776\s+2167\s+\n/
//

ID infoseq-ex4
UC Display only the description of a sequence:
AP infoseq
CL tembl:x13776 -only -desc
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 88
FP /^Pseudomonas aeruginosa .* regulation\n/
//

ID infoseq-ex5
UC Display the type of a sequence:
AP infoseq
CL tembl:x13776 -only -type
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 12
FP /^Type\s+\nN\s+\n/
//

ID infoseq-ex6
UC Display information formatted with HTML:
AP infoseq
CL tembl:x13776 -html
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 432
FP /^<tr><td>tembl-id:X13776</td><td>tembl</td><td>X13776</td><td>X13776</td><td>N</td><td>2167</td><td>66\.54</td><td>Pseudomonas .* regulation</td></tr>\n/
//

ID isochore-ex
AP isochore
CL tembl:AF129756  -graph cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI af129756.iso
FZ = 22819
FP /^5000\s+0\.476\n/
FI isochore.ps
FZ > 100
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI stdout
FZ = 20
FP /^Created isochore\.ps\n/
//


ID jaspextract-keep
AP jaspextract
DL keep
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
IN ../../data/jaspar
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI JASPAR_CNE
DI JASPAR_CORE
DF MA0070.1.pfm
DF MA0071.1.pfm
DF MA0072.1.pfm
DF MA0073.1.pfm
DF MA0074.1.pfm
DF MA0075.1.pfm
DF MA0076.1.pfm
DF MA0077.1.pfm
DF MA0078.1.pfm
DF MA0079.1.pfm
DF matrix_list.txt
DI JASPAR_FAM
DI JASPAR_PBM
DI JASPAR_PBM_HLH
DI JASPAR_PBM_HOMEO
DI JASPAR_PHYLOFACTS
DI JASPAR_POLII
DI JASPAR_SPLICE
//

ID jaspscan-ex
AP jaspscan
PP EMBOSS_DATA=../jaspextract-keep/
PP export EMBOSS_DATA
CL -both
IN tembl:m23100
IN
IN ma0079.1
IN
IN
FI stderr
FC = 12
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI m23100.jaspscan 
FC = 42
FP /^ +117 +126 +[+] +82.143 +MA0079[.]1 +SP1 +9606 +Zinc-coordinating/
FP 12 /^ +\d+ +\d+ +[+]/
FP 6 /^ +\d+ +\d+ +[-]/
//

ID jembossctl-ex
CC for jemboss installations
CC can only be run through tomcat so simply exits here
AP jembossctl
CL jctl.file
ER 255
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

# remove the extra 2 prompts from the example
ID lindna-ex
AP lindna
CL -graph cps
IN ../../data/data.linp
IN
IN
FI stdout
FZ = 18
FP /^Created lindna\.ps\n/
FI stderr
FC = 5
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI lindna.ps
FC = 285
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

## Example should be file1 file2
ID listor-ex
UC Write the logical OR of two lists:
AP listor
CL ../../data/file1 ../../data/file2
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI file1.list
FZ = 115
FC = 4
FP 4 /^fasta::/
FP 3 /file1/
FP 1 /file2/
//

ID listor-ex2
UC Write the logical AND of two lists:
AP listor
CL ../../data/file1 ../../data/file2 -operator and
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI file1.list
FZ = 58
FC = 2
FP 2 /^fasta::/
FP 2 /file1/
FP 0 /file2/
//

ID listor-ex3
UC Write the logical XOR of two lists:
AP listor
CL ../../data/file1 ../../data/file2 -operator xor
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI file1.list
FZ = 57
FC = 2
FP 2 /^fasta::/
FP 1 /file1/
FP 1 /file2/
//

ID listor-ex4
UC Write the logical NOT of two lists:
AP listor
CL ../../data/file1 ../../data/file2 -operator not
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI file1.list
FZ = 28
FC = 1
FP 1 /^fasta::/
FP 1 /file1/
FP 0 /file2/
FP 1 /file1:one/
//

ID makenucseq-ex
AP makenucseq
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI makeseq.fasta
FC = 300
FP 100 /^>EMBOSS_[0-9][0-9][0-9]/
FP /\A>EMBOSS_001\nggtccgaggggta.*gataaaa\ntaaaatg.*cccta\n/
//

ID makenucseq-ex2
UC Providing a codon usage file specifies the sequence composition.
UC This Pseudomonas aeruginosa file specifies a high GC content.
AP makenucseq
IN Epseae.cut
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI makeseq.fasta
FC = 300
FP 100 /^>EMBOSS_[0-9][0-9][0-9]/
FP /\A>EMBOSS_001\ngggcgtctg.*gtcaacttc\ngcgcggcag.*gtgcgcg\n/
//

ID makeprotseq-ex
AP makeprotseq
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI makeseq.fasta
FC = 300
FP 100 /^>EMBOSS_[0-9][0-9][0-9]/
FP /\A>EMBOSS_001\nnrvlhpepnprt.*lmmydsqfwcdfe\nwadcc.*gkkvd\n>/
//

ID marscan-ex
AP marscan
IN tembl:u01317
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI u01317.marscan 
FZ = 1413
FP /\t2242\t2458\t.*start8bp 2451;.*end8bp 2458;.*start16bp 2242;.*end16bp 2257\n/
//

ID maskambignuc-ex
AP maskambignuc
IN ../../data/ambignuc.fasta
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ambignuc.fasta
FC = 2
FP /^ANCNGNNNNNNTUNNNancngnnnnnntunnn\n/
//

ID maskambigprot-ex
AP maskambigprot
IN ../../data/ambigprot.fasta
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ambigprot.fasta
FC = 2
FP /^AXCDEFGHIXKLMNXPQRSTXVWXYXXaxcdefghixklmnxpqrstxvwxyxX\n/
//

ID maskfeat-ex
UC Mask out a feature whose type is "repeat_region" from position 2331 to 2356:
AP maskfeat
CL tembl:ab000360
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ab000360.fasta
FZ = 2685
FP /^>AB000360 /
FP /^NNNNNNNNNNNNNNNNaaagtcacttctttctacccttttcaatgtgctaatgctctttt\n/
//

ID maskfeat-ex2
UC Change to lower-case a feature whose type is "repeat_region" from position 2331 to 2356. Note that '-supper' is used to make the whole sequence upper-case before the lower-case masking:
AP maskfeat
CL tembl:ab000360 -tolower -supper
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ab000360.fasta
FZ = 2685
FP /^>AB000360 /
FP /^gtgtgtgtgtgtgtgtAAAGTCACTTCTTTCTACCCTTTTCAATGTGCTAATGCTCTTTT\n/
//

ID maskseq-ex
UC Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq':
AP maskseq
CL ../../data/prot.fasta prot2.seq -reg=10-12
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI prot2.seq
FZ = 146
FP /^ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\n/
//

ID maskseq-ex2
UC Mask off bases 20 to 30 from a sequence 'prot.fasta' using the character 'x' and write to the new sequence file 'prot2.seq': 
AP maskseq
CL ../../data/prot.fasta prot2.seq -reg=20-30 -mask=x
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI prot2.seq
FZ = 146
FP /^ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\n/
//

ID maskseq-ex3
UC Mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':
AP maskseq
CL ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI prot2.seq
FZ = 146
FP /^ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY\n/
FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY\n/
//

ID maskseq-ex4
UC Change to lower-case the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':
AP maskseq
CL ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 -tolower
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI prot2.seq
FZ = 146
FP /^ACDEFGHIKLMNPQRSTVWyacdEFGHIKLMNPqrstvwyacdefGHIKLMNPQRSTVWY\n/
FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHiklMNPQRSTVWY\n/
//

ID maskseq-userange
UC Change to lower-case the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':
AP maskseq
CL ../../data/prot.fasta prot2.seq -reg='20,+4,34-45,88+3' -tolower
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI prot2.seq
FZ = 146
FP /^ACDEFGHIKLMNPQRSTVWyacdEFGHIKLMNPqrstvwyacdefGHIKLMNPQRSTVWY\n/
FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHiklMNPQRSTVWY\n/
//

ID matcher-ex
AP matcher
CL tsw:hba_human tsw:hbb_human
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.matcher
FP /^# Identity: +63\/145 \(43\.4%\)/
FP /^# Score: +264\n/
FP /^HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP\n/
FC = 49
//

ID matcher-ex2
UC To find the 10 best alignments:
AP matcher
CL tsw:hba_human tsw:hbb_human -alt 10
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.matcher
FP /^# Identity: +63\/145 \(43\.4%\)/
FP /^# Score: +264\n/
FP /^HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP\n/
FC = 275
//

ID megamerger-ex
TI 300
AP megamerger
CL tembl:v00295 tembl:v00296
IN
IN
IN report
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI report
FC = 15
FP /^V00295 overlap starts at 1\n/
FP /^V00296 overlap starts at 3019\n/
FI v00295.merged
FZ = 4659
FP /^tgtcaaaaataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaatcc\n/
FP /^ggcttaccggaaaaaaga\n/
//

ID merger-ex
AP merger
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FZ > 1445
FP /^# Score: 795\.0\n/
FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/
FP /^X51872 +1 [-]+gtgaatgaa +9\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID msbar-ex
UC This asks for 5 mutations, with point mutations as changes (substitutions), and the codon and block mutations ignored.
AP msbar
IN tembl:j01636
IN 5
IN 4
IN
IN
IN
FI stderr
FC = 26
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
##
## hard to test - different changes each time
FI j01636.fasta 
FZ = 7679
FP /^>J01636 J01636/
//

ID mwcontam-ex
AP mwcontam
IN ../../data/mw1.dat,../../data/mw2.dat,../../data/mw3.dat
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.mwcontam
FZ = 15
FP /^67\.000\n/
FP /^415\.000\n/
//

ID mwfilter-ex
AP mwfilter
IN ../../data/molwts.dat
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI molwts.mwfilter
FZ = 190
FC = 16
FP /^874\.364756\n/
//

ID needle-ex
AP needle
CL tsw:hba_human tsw:hbb_human
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.needle 
FZ > 1270
FP /^# Score: 292\.5\n/
FP /HBB_HUMAN +1 +MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD +48\n/
FP /HBA_HUMAN +49 +LS-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR +93\n/
//

ID needleall-ex
AP needleall
CL -minscore 40 -stdout -auto
CL ../../data/illumina_adapter_primer.fa
CL ../../data/test1_illumina.fastq
FI stderr
FI needleall.error
FP /Alignment score \(21.5\) is less than minimum score/
FC = 752
FI stdout
FC = 26
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FZ > 1270
FP /^Illumina_DpnII_Gex_PCR_Primer_2.*(41.0)/
//

ID newcpgreport-ex
AP newcpgreport
IN tembl:u68037
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI u68037.newcpgreport
FZ = 540
FP /^FT   CpG island       104\.\.509\n/
FP /^FT                    \/size=406\n/
FP /^FT                    \/Sum C\+G=269\n/
FP /^FT                    \/Percent CG=66\.26\n/
FP /^FT                    \/ObsExp=0\.81\n/
FP /^FT   CpG island       596\.\.924\n/
FP /^FT   numislands       2\n/
//

ID newcpgseek-ex
AP newcpgseek
IN tembl:u68037
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI u68037.newcpgseek
FZ = 277
FP /^with score \> 17 \n/
FP /^\*    96   1032   630         87  66\.1   0\.65\n/
FP /^  1072   1100    26          3  62\.1   0\.00\n/
FP /^  1183   1193    26          2  72\.7   2\.00\n/
//

# example to use SWISS format (for protein)
ID newseq-ex
UC Type in a short sequence to the file 'mycc.pep' in SWISSPROT format:
AP newseq
IN cytoc
IN fragment of cytochrome c
IN p
IN KKKEERADLIAY
IN swiss::mycc.pep
FI stderr
FC = 5
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI mycc.pep
FZ = 167
FP /^ID   cytoc                   Unreviewed;          12 AA\.\n/
FP /^DE   fragment of cytochrome c\n/
FP /^SQ   SEQUENCE   12 AA;  1464 MW;  6F142FA88DADC40B CRC64;/
//

ID nohtml-ex
AP nohtml
IN ../../data/webfile.html
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI webfile.nohtml
FC = 10
FP /^embossdata\n/
FP 5 /^.*\S+.*\n/
//

ID noreturn-ex
AP noreturn
CL ../../data/abc.dat
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI abc.noreturn
FZ = 71
FP /carriage return format\nACDEFGHIKLMNPQRSTVWY\n$/
//

ID noreturn-topc
AP noreturn
CL ../../data/abc.dat -system pc
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI abc.noreturn
FZ = 73
FP /carriage return format\r\nACDEFGHIKLMNPQRSTVWY\r\n$/
//

ID noreturn-tomac
AP noreturn
CL ../../data/abc.dat -system mac
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI abc.noreturn
FZ = 71
FP /carriage return format\rACDEFGHIKLMNPQRSTVWY\r$/
//


ID nospace-ex
AP nospace
IN ../../data/seqspace.txt
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI seqspace.nospace
FC = 46
FP /^>X13776\n/
FP /^ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacggga\n/
//


ID notab-ex
AP notab
IN ../../data/tabfile.txt
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI tabfile.notab
FC = 9
FP /^a       b       c       d\n/
FP /^ab      cd      ef      g\n/
FP /^abc     def     ghi     j\n/
FP /^abcd    efgh    ijkl    m\n/
FP /^abcde   fghij   klmno   p\n/
FP /^abcdef  ghijkl  mnopqr  s\n/
FP /^abcdefg hijklmn opqrstu v\n/
FP /^abcdefgh        ijklmnop\n/
//
# change example to use globins.fasta
ID notseq-ex
UC In this case the excluded sequences (myg_phyca and lgb2_luplu) are not saved to any file:
AP notseq
IN ../../data/globins.fasta
IN myg_phyca,lgb2_luplu
IN mydata.seq
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI mydata.seq
FZ = 926
FP /^>HBA_HUMAN/
FP /^>HBA_HORSE/
FP /^>HBB_HUMAN/
FP /^>HBB_HORSE/
FP /^>GLB5_PETMA/
FP 0 /^>MYG_PHYCA/
FP 0 /^>LGB2_LUPLU/
//

ID notseq-ex2
UC Here is an example where the sequences to be excluded are saved to another file:
AP notseq
CL -junkout hb.seq
IN ../../data/globins.fasta
IN hb*
IN mydata.seq
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI mydata.seq
FZ = 581
FP 0 /^>HBA_HUMAN/
FP 0 /^>HBA_HORSE/
FP 0 /^>HBB_HUMAN/
FP 0 /^>HBB_HORSE/
FP /^>GLB5_PETMA/
FP /^>MYG_PHYCA/
FP /^>LGB2_LUPLU/
FI hb.seq
FP /^>HBB_HUMAN/
//

ID nthseq-ex
AP nthseq
IN @../../data/eclac.list
IN 2
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.fasta
FZ = 1942
FP /^>X51872 X51872\.1 Escherichia coli lacA gene/
//

ID nthseqset-ex
AP nthseqset
CL -osf phylip
IN ../../data/globins-all.phy
IN 2
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins-all.phylip
FZ = 1578
FP 1 /^ 7 167\n/
FP /^          FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF\n/
//

ID octanol-ex
AP octanol
IN tsw:opsd_human
IN ps
FI stdout
FZ = 19
FP /^Created octanol\.ps\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI octanol.ps
FC = 302
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID octanol-nodiff
AP octanol
CL -noplotdiff
IN tsw:opsd_human
IN ps
FI stdout
FZ = 19
FP /^Created octanol\.ps\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI octanol.ps
FC = 262
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID oddcomp-ex
UC To search for entries in swissprot with at least 1 SR AND at least 2 RS:
AP oddcomp
IN tsw:*
IN ../../data/oddcomp.comp
IN
IN out.odd
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI out.odd
FP /CNR1B_TAKRU/
FZ = 186
//

ID ontocount-ex
AP ontocount
CL edam:1234
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^1\n/
//

ID ontocount-ex2
AP ontocount
CL edam:1234 -subclasses
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^5\n/
//

ID ontoget-ex
AP ontoget
CL edam:1234
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 1234.obo
FP /^id: EDAM_data:1234\n/
FP 1 /^id: /
FP 1 /^is_a: EDAM_data:0850/
FP 0 /^relationship: /
FC = 12
//

ID ontoget-ex2
AP ontoget
CL edam:0850 -subclasses
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 0850.obo
FP /^id: EDAM_data:1234\n/
FP 12 /^id: /
FP 4 /^is_a: EDAM_data:0850/
FP 2 /^is_a: EDAM_data:1235/
FP 3 /^relationship: /
FC = 151
//

ID ontogetcommon-ex
AP ontogetcommon
CL "edam:{0097,0640}"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ontogetcommon.obo
FC = 16
FP /^id: EDAM_topic:0077\n/
FP 1 /^id: /
//

ID ontogetdown-ex
AP ontogetdown
CL edam:0850
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 0850.obo
FP /^id: EDAM_data:1234\n/
FP 4 /^id: /
FP 4 /^is_a: EDAM_data:0850/
FP 2 /^relationship: /
FC = 49
//

ID ontogetobsolete-ex
AP ontogetobsolete
CL edam:alignment -subclasses
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 1916.obo
FP /^id: EDAM_topic:0083\n/
FP 1 /^id: /
FP 1 /^consider: EDAM_topic:0182/
FP 1 /^consider: EDAM_topic:0183/
FP 0 /^relationship: /
FC = 15
//

ID ontogetroot-ex
AP ontogetroot
CL edam:1234
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 1234.obo
FP /^id: EDAM_data:0006\n/
FP 1 /^id: /
FP 0 /^relationship: /
FP 0 /^is_a: /
FC = 24
//

ID ontogetsibs-ex
AP ontogetsibs
CL edam:0575
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 0575.obo
FP /^id: EDAM_operation:0575\n/
FP 3 /^id: /
FP 2 /^relationship: /
FC = 36
//

ID ontogetup-ex
AP ontogetup
CL edam:1234
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 1234.obo
FP /^id: EDAM_data:0850\n/
FP /^id: EDAM_data:2977\n/
FP 2 /^id: /
FP 0 /^relationship: /
FC = 25
//

ID ontoisobsolete-ex
AP ontoisobsolete
CL edam:0195
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^Obsolete\n/
FC = 1
//

ID ontoisobsolete-ex2
AP ontoisobsolete
CL edam:0575
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^EDAM_operation:0575 OK\n/
FC = 1
//

ID ontotext-ex
AP ontotext
CL edam:1234
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 1234.ontotext
FP /^id: EDAM_data:1234\n/
FP 1 /^id: /
FP 1 /^is_a: EDAM_data:0850/
FP 0 /^relationship: /
FC = 12
//

ID ontotext-ex2
AP ontotext
CL edam:0850 -subclasses
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 0850.ontotext
FP /^id: EDAM_data:1234\n/
FP 12 /^id: /
FP 4 /^is_a: EDAM_data:0850/
FP 2 /^is_a: EDAM_data:1235/
FP 3 /^relationship: /
FP 0 /^!/
FC = 151
//

ID palindrome-ex
AP palindrome
IN tembl:d00596
IN 15
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI d00596.pal
FZ = 1579
FP /^Palindromes:\n126 +caaaaaaaaaaaaaaaa +142\n/
FP /^217 +gtttttttttttttttt +201\n/
FP /^127 +aaaaaaaaaaaaaaaagaccgccagggct +155\n/
FP /^204 +ttttttttttttttttctggcggtcccga +176\n/
//

# change the examples to use these files
ID pasteseq-ex
UC To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta': 
AP pasteseq
CL tsw:amir_pseae tsw:flav_nossm -pos=67
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir_pseae.fasta
FZ = 275
FP /^FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL\n/
//

ID pasteseq-ex2
UC This does the same thing, but the output qualifier is explicitly used:
AP pasteseq
CL tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amirplus.seq
FZ = 275
FP /^FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL\n/
//

ID pasteseq-ex3
UC To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0:
AP pasteseq
CL tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amirplus.seq
FZ = 275
FP /^DALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVAL\n/
//

ID patmatdb-ex
AP patmatdb
IN tsw:*
IN st[ty]s
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cru4_arath.patmatdb 
FC = 80
FP /^# Sequence: HD_TAKRU     from: 1   to: 3148\n# HitCount: 1\n/
FP /^Length = 4\n/
FP /^Start = position 1038 of sequence\n/
FP /^End = position 1041 of sequence\n/
FP /^STPASSTTSSAVDP\n/
FP /^# Reported_sequences: 3\n/
FP /^# Reported_hitcount: 3\n/
//

ID pepcoil-ex
AP pepcoil
IN tsw:gcn4_yeast
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI gcn4_yeast.pepcoil 
FZ = 845
FP 1 /^ +Sequence:/
FP /^\(1\) Score 1\.910 length 49 at residues 233->281\n/
FP /^ Sequence: ARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER\n/
OC The SwissProt annotation marks the true leucine zipper motif as from 253 to 274.
OC The leucine zipper is a special case of a coiled-coil region.
//

ID pepdigest-ex
AP pepdigest
IN tsw:opsd_human
IN
IN
IN
FI stderr
FC = 11
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI opsd_human.pepdigest
FP /^    246     248    346\.384 K      E      AEK\n/
FP /yields 14 fragments/
FC = 36
//

ID pepdigest-range
AP pepdigest
CL -sbegin 10 -send 250
IN tsw:opsd_human
IN
IN
IN
FI stderr
FC = 11
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI opsd_human.pepdigest
FP /^    246     248    346\.384 K      E      AEK\n/
FP /yields 8 fragments/
FC = 32
//

ID pepinfo-ex
AP pepinfo
IN tsw:opsd_human
IN cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created pepinfo\.ps\n/
FI opsd_human.pepinfo 
FC = 4248
FP 3 /^\s+4\s+T\s+1\n/
FP 6 /^\s+4\s+T\s+0\n/
FP 3 /^\s+4\s+T\s+0\.000\n/
FI pepinfo.ps
FC = 23209
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 2\n/
//

ID pepinfo-plot1
AP pepinfo
CL -nohydropathyplot
IN tsw:opsd_human
IN cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created pepinfo\.ps\n/
FI opsd_human.pepinfo 
FC = 3186
FP 3 /^\s+4\s+T\s+1\n/
FP 6 /^\s+4\s+T\s+0\n/
FP 0 /^\s+4\s+T\s+0\.000\n/
FI pepinfo.ps
FC = 22594
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepinfo-plot2
AP pepinfo
CL -nogeneralplot
IN tsw:opsd_human
IN cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created pepinfo\.ps\n/
FI opsd_human.pepinfo 
FC = 1062
FP 0 /^\s+4\s+T\s+1\n/
FP 0 /^\s+4\s+T\s+0\n/
FP 3 /^\s+4\s+T\s+0\.000\n/
FI pepinfo.ps
FC = 709
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepnet-ex
AP pepnet
CL -sask
IN tsw:gcn4_yeast
IN 253
IN 274
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 18
FP /^Created pepnet\.ps\n/
FI pepnet.ps
FC = 447
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepnet-data
AP pepnet
CL -sask -graph data
## No -outfile qualifier - fixed filename
IN tsw:gcn4_yeast
IN 253
IN 274
FI stdout
FC = 1
FP /^Created pepnet1\.dat\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pepnet1.dat
FC = 105
FP /^##Maintitle Helical net of tsw-id:GCN4_YEAST\[253:274\]\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^Text1 x1 139\.599991 y1 93\.500000 colour 1 size 0\.750000 D\n/
FP /^Rectangle x1 134\.499985 y1 85\.430000 x2 137\.499985 y2 88\.430000 colour 9\n/
//

ID pepstats-keep
AP pepstats
DL keep
IN tsw:laci_ecoli
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.pepstats
FZ = 1568
FP /^Molecular weight = 38590\.16/
FP /^Average Residue Weight  = 107\.195\s+Charge\s+= 1\.5\s+\n/
FP /^Isoelectric Point = 6\.8385\n/
FP /^A280 Molar Extinction .*  = 22920 .* 23045 /
FP /^A280 Extinction .* = 0\.594 .* 0\.597 /
FP /^Improbability of expression in inclusion bodies = 0\.660\n/
FP /^A = Ala\s+44\s+12\.222\s+1\.421\s+\n/
FP /^Tiny\s+\(A\+C\+G\+S\+T\)\s+120\s+33\.333\n/
//

ID pepstats-expasy
AP pepstats
DL keep
CL -pkdata Epkexpasy.dat
IN tsw:laci_ecoli
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.pepstats
FZ = 1568
FP /^Molecular weight = 38590\.16/
FP /^Average Residue Weight  = 107\.195\s+Charge\s+= 1\.5\s+\n/
FP /^Isoelectric Point = 6\.3901\n/
FP /^A280 Molar Extinction .*  = 22920 .* 23045 /
FP /^A280 Extinction .* = 0\.594 .* 0\.597 /
FP /^Improbability of expression in inclusion bodies = 0\.660\n/
FP /^A = Ala\s+44\s+12\.222\s+1\.421\s+\n/
FP /^Tiny\s+\(A\+C\+G\+S\+T\)\s+120\s+33\.333\n/
//

ID pepstats-innovagen
AP pepstats
DL keep
CL -pkdata Epkinnovagen.dat
IN tsw:laci_ecoli
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.pepstats
FZ = 1568
FP /^Molecular weight = 38590\.16/
FP /^Average Residue Weight  = 107\.195\s+Charge\s+= 1\.5\s+\n/
FP /^Isoelectric Point = 6\.4206\n/
FP /^A280 Molar Extinction .*  = 22920 .* 23045 /
FP /^A280 Extinction .* = 0\.594 .* 0\.597 /
FP /^Improbability of expression in inclusion bodies = 0\.660\n/
FP /^A = Ala\s+44\s+12\.222\s+1\.421\s+\n/
FP /^Tiny\s+\(A\+C\+G\+S\+T\)\s+120\s+33\.333\n/
//

ID makeprotseq-ex2
AP makeprotseq
IN ../pepstats-keep/laci_ecoli.pepstats
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI makeseq.fasta
FC = 300
FP 100 /^>EMBOSS_[0-9][0-9][0-9]/
FP /\A>EMBOSS_001\neqngievef.*avpdkallvv\nnllvla.*kssnv\n>/
//

ID pepwheel-ex
AP pepwheel
CL tsw:hbb_human -send 30
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 20
FP /^Created pepwheel\.ps\n/
FI pepwheel.ps
FC = 575
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepwheel-data
AP pepwheel
CL tsw:hbb_human -send 30 -graph data
FI stdout
FC = 1
FP /^Created pepwheel1\.dat\n/
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pepwheel1.dat
FC = 132
FP /^##Maintitle Helical wheel of tsw-id:HBB_HUMAN\[:30\]\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^Text1 x1 0\.249452 y1 -0\.043985 colour 9 size 1\.000000 V\n/
FP /^Rectangle x1 0\.224452 y1 -0\.065985 x2 0\.274452 y2 -0\.015985 colour 9\n/
//

ID pepwindow-ex
AP pepwindow
CL tsw:opsd_human
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 21
FP /^Created pepwindow\.ps\n/
FI pepwindow.ps
FC = 305
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepwindow-local
AP pepwindow
PP EMBOSS_DATA=../aaindexextract-keep/
PP export EMBOSS_DATA
CL tsw:opsd_human
IN ps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 21
FP /^Created pepwindow\.ps\n/
FI pepwindow.ps
FC = 305
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepwindow-localdata
AP pepwindow
PP EMBOSS_DATA=../aaindexextract-keep/
PP export EMBOSS_DATA
CL tsw:opsd_human -datafile chop780101
IN ps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 21
FP /^Created pepwindow\.ps\n/
FI pepwindow.ps
FC = 317
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID pepwindow-localfail
AP pepwindow
ER 1
PP EMBOSS_DATA=../aaindexextract-keep/
PP export EMBOSS_DATA
CL tsw:opsd_human -datafile fail780101
IN ps
FI stderr
FC = 3
FP /^Error: Unable to open data file 'fail780101' for input\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

# change example to globins.msf (plural)
ID pepwindowall-ex
AP pepwindowall
CL ../../data/globins.msf -gxtitle="Base Number" -gytitle="hydropathy"
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 24
FP /^Created pepwindowall\.ps\n/
FI pepwindowall.ps
FC = 456
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

# change example to use globins.msf
ID plotcon-ex
AP plotcon
CL -sformat msf ../../data/globins.msf -graph cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created plotcon\.ps\n/
FI plotcon.ps
FC = 257
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID plotcon-data
AP plotcon
CL -sformat msf ../../data/globins.msf -graph data
IN
FI stdout
FC = 1
FP /^Created plotcon1\.dat\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI plotcon1.dat
FC = 179
FP /^##Points 164\n/
FP /^135\.000000\s+0\.305580\n/
//

ID plotorf-ex
AP plotorf
IN tembl:x13776
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created plotorf\.ps\n/
FI plotorf.ps
FC = 741
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID plotorf-ex2
UC An example of specifying your own START and STOP codons with a mitochondrial sequence would be:
AP plotorf
CL -start ATT,ATC,ATA,ATG,GTG -stop TAA,TAG,AGA,AGG
IN ../../data/mito.seq
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created plotorf\.ps\n/
FI plotorf.ps
FC = 6352
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID polydot-ex
AP polydot
CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta"
CL -graph cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created polydot\.ps\n/
FI polydot.ps
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID polydot-data
AP polydot
CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta"
CL -graph data
IN
FI stdout
FC = 1
FP /^Created polydot1\.dat\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI polydot1.dat
FC = 202
FP /^##Maintitle Polydot of globins.fasta\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^##Screen x1 -163\.350006 y1 -163\.350006 x2 1690\.672485 y2 1252\.349976\n/
FP /^Textline x1 -98\.010010 y1 73\.000000 x2 -98\.010010 y2 146\.000000 colour 0 size 0\.300000 HBB_HUMAN\n/
FP /^Rectangle x1 0\.000000 y1 156\.000000 x2 146\.000000 y2 302\.000000 colour 0\n/
FP /^Text1 x1 1121\.670044 y1 1056\.329956 colour 0 size 0\.300000 No\. Length  Lines  Points Sequence\n/
FP /^Text1 x1 1121\.670044 y1 1023\.659973 colour 0 size 0\.300000   1    146     8    248 HBB_HUMAN\n/
//

ID polydot-feat
AP polydot
CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta"
CL -graph cps -dumpfeat
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created polydot\.ps\n/
FI polydot.ps
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
FI globins.gff
FC = 63
FP 7 /^##sequence-region /
FP /HBB_HUMAN\s+wordmatch\s+polypeptide_region\s+88\s+111\s+1\s+[.]\s+\.\s+ID=HBB_HUMAN\.1;note=HBB_HORSE\n/
//

ID preg-ex
AP preg
IN tsw:*_rat
IN IA[QWF]A
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI arf3_rat.preg
FC = 31
FP /^   2289    2292 regex:IA\[QWF\]A IAQA\n/
FP /^# Total_sequences: 2\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 1\n/
//

ID prettyplot-ex
AP prettyplot
CL -blocksperline=5 -boxcol -consensus -ratio=0.59
IN ../../data/globins.msf
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 22
FP /^Created prettyplot\.ps\n/
FI prettyplot.ps
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID prettyplot-ex2
AP prettyplot
CL ../../data/globins.msf -ratio=0.59 -docolour
IN cps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 22
FP /^Created prettyplot\.ps\n/
FI prettyplot.ps
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID prettyplot-data
AP prettyplot
CL -blocksperline=5 -boxcol -consensus -ratio=0.59
CL -graph data
IN ../../data/globins.msf
FI stdout
FC = 4
FP /^Created prettyplot2\.dat\n/
FP 4 /^Created prettyplot\d\.dat\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI prettyplot1.dat
FC = 603
FP /^##Maintitle Pretty plot of ..\/..\/data\/globins.msf\n/
FP /^##Subtitle Mon 15 Jul 2013 12:00:00\n/
FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/
FP /^Text1 x1 -10\.000000 y1 36\.619671 colour 0 size 10\.491803 Consensus\n/
FP /^Text1 x1 59\.000000 y1 36\.619671 colour 0 size 10\.491803 50\n/
FP /^Text2 x1 18\.500000 y1 36\.619671 colour 0 size 10\.491803 S\n/
FI prettyplot2.dat
FC = 862
FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/
FP /^Text2 x1 1\.500000 y1 36\.619671 colour 0 size 10\.491803 F\n/
FI prettyplot3.dat
FC = 815
FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/
FP /^Text2 x1 2\.500000 y1 36\.619671 colour 0 size 10\.491803 H\n/
FI prettyplot4.dat
FC = 181
FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/
FP /^Text2 x1 3\.500000 y1 36\.619671 colour 0 size 10\.491803 L\n/
//

ID prettyseq-ex
AP prettyseq
IN tembl:x13776
IN 135-1292
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.prettyseq 
FZ = 8166 
FP / 121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180\n/
FP / 1               M  G  S  H  Q  E  R  P  L  I  G  L  L  F  S  E 16\n/
//

ID primersearch-ex
AP primersearch
CL tembl:z52466
IN ../../data/primers
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI z52466.primersearch
FZ = 402
FP /^Primer name D1S2660\nAmplimer 1\n/
FP /^\tSequence: Z52466 Z52466 \n/
FP /^\tH\.sapiens \(D1S2660\) DNA segment containing \(CA\) repeat; clone AFMa203yc1; single read\.\n/
FP /^\tCACACATGCACATGCAC hits forward strand at 27 with 0 mismatches\n/
FP /^\tAGTGACACCAGCAGGG hits reverse strand at \[103\] with 0 mismatches\n/
FP /^\tAmplimer length: 261 bp\n/
//

ID primersearch-ex2
UC Here we run the same example but allowing 20% mismatch between the primers and the sequence:
AP primersearch
CL tembl:z52466
IN ../../data/primers
IN 20
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI z52466.primersearch
FZ = 680
FP /^Amplimer 1\n\tSequence: Z52466 Z52466 \n/
FP /^Amplimer 2\n\tSequence: Z52466 Z52466 \n/
FP /^\tCACACATGCACATGCAC hits forward strand at 49 with 2 mismatches\n/
//

## commit a data/seqs.list file for input

##ID primersearch-ex3
##UC Here is an example of running with a file containing a list of sequences:
##CC Need the seqs.list input list
##AP primersearch
##CL @../../data/seqs.list
##IN ../../data/primers
##IN
##IN
##FI stderr
##FC = 2
##FP 0 /Warning: /
##FP 0 /Error: /
##FP 0 /Died: /
##FI hs214yg7.primersearch
##FZ = 0
##//

ID printsextract-keep
DL keep
PP mkdir ./PRINTS
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
AP printsextract
IN ../../data/prints.test
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI PRINTS
//


ID profit-ex
AP profit
## changed to a matrix file which produces some results
##IN ../../data/globins.prophecy
IN ../../data/outfile.prophecy
IN tsw:*
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.profit
FZ = 180
FP /^HBB_HUMAN/
//

ID prophecy-ex
AP prophecy
IN ../../data/globins.msf
IN
IN globins
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.prophecy 
FZ = 13782
FC = 173
FP /^Maximum score\s+496\n/
FP /^Consensus\s+PIVDT.*AAYQG\n/
//

ID prophecy-ex2
AP prophecy
IN ../../data/globins.msf
IN g
IN
IN globins
IN
IN
IN
FI stderr
FC = 6
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.prophecy 
##
## Do not check file size. AIX reports -0.00 in some positions
## so the file can be slightly larger
##
FP /^Max_score\s+939\.76\n/
FP /^Consensus\s+PIVDT.*ELGYQG\n/
FP /^0\.65 0\.00 0\.13 0\.13 0\.13 -0\.78 .* 0\.87 0\.87\n/
//

# example - use h* to save time
ID prophet-ex
TI 600
AP prophet
IN tsw:h*
IN ../../data/globins.gribskov
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.prophet
FP /^# Score: 161\.14\n/
FP /^globins +15 ELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLS +64\n/
FP /^HBA_HUMAN +2 VLSPADKTNVKAAW-GKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS +50\n/
//

ID prosextract-keep
AP prosextract
DL keep
PP mkdir ./PROSITE
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
IN ../../data/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI PROSITE
//

ID patmatmotifs-ex
AP patmatmotifs
PP EMBOSS_DATA=../prosextract-keep/
PP export EMBOSS_DATA
CL -full
IN tsw:opsd_human
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI opsd_human.patmatmotifs
FP /^# HitCount: 2\n/
FP /^# Motif: OPSIN\n# Count: 1\n/
FP /^Start = position 123 of sequence\n/
FP /^End = position 139 of sequence\n/
FP /^Length = 17\n/
FP /^Motif = G_PROTEIN_RECEP_F1_1\n/
FP /^TLGGEIALWSLVVLAIERYVVVCKPMS\n/
//

ID pscan-ex
AP pscan
PP EMBOSS_DATA=../printsextract-keep/
PP export EMBOSS_DATA
IN tsw:opsd_human
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI opsd_human.pscan 
FZ = 871
FP /^Fingerprint GPCRRHODOPSN Elements 7\n    Accession number PR00237\n/
FP /^  Element 2 Threshold 49% Score 75%\n/
FP /^             Start position 72 Length 22\n/
FP /^  Element 1 Threshold 54% Score 64%\n/
FP /^             Start position 39 Length 25\n/
//

ID psiphi-ex
AP psiphi
CL ../../data/1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 1hmp_a.psiphi 
FZ = 3843
FP /     56      56     0\.0 \-139\.15  162\.01\n/
//

ID rebaseextract-keep
AP rebaseextract
DL keep
PP mkdir ./REBASE
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
IN ../../data/withrefm
IN ../../data/proto
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
DI REBASE
DF embossre.enz
DF embossre.equ
DF embossre.ref
DF embossre.sup
//

ID recoder-ex
AP recoder
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
IN tembl:x65923
IN EcoRII
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.recoder
FC = 59
FP 3 / +77 +81 +[+] +EcoRII +CCWGG +78 +P\.P +C->[ACGT]\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 22\n/
//

ID recoder-seqs
AP recoder
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
CL -sshow -tshow
IN tembl:x65923
IN EcoRII
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.recoder
FC = 79
FP 3 / +77 +81 +[+] +EcoRII +CCWGG +78 +P\.P +C->[ACGT]\n/
FP /# 61 +AGCTCTTTGT CCGCGCCCAG GAGCTACACA CCTTCGAGGT GACCGGCCAG GAAACGGTCG \n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 22\n/
//

# make bamhi explicit in reply to prompt
ID redata-ex
AP redata
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
IN BamHI
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.redata
FP /\ABamHI\n/
FP /^Recognition site is GGATCC leaving sticky ends\n/
FP /^  Cut positions 5':1 3':5\n/
//

ID refseqget-ex
AP refseqget
CL -of embl
IN tembl:em498477
IN test.out
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 37
FP /     aattatttat attatggtat gagattagct cgtactcaag atggtggcac aaattatNNN       900\n/
FP /     NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNta tgctagatta       960\n/
FP /     cacacttgtt gatttaacag catttgattc tggtacacat agtattacag c               1791\n/
//

ID remap-ex
UC This example uses only a small region of the input sequence to save space.
UC This is run with a small test version of the restriction enzyme database
UC and so you will probably see more enzymes when you run this.
AP remap
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
CL -notran -sbeg 1 -send 60
IN tembl:j01636
IN taqi,bsu6i,acii,bsski
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.remap 
FZ = 1228
FP /^# Enzymes that cut.*\n(\s+\S+\s+1\s+\S*\n){4}\n/
FP /^# Enzymes that do not cut.*\n\n/
FP /^\s+AciI\s+1\s+\n/
FP /^\s+BssKI\s+1\s+\n/
FP /^\s+Ksp632I\s+1\s+Bsu6I\n/
FP /^\s+TaqI\s+1\s+\n/
//

ID remap-ex2
UC This is an example where all enzymes in the REBASE database are used,
UC (but only the prototypes of the isoschizomers are reported by default).
UC This is run with a small test version of the restriction enzyme database
UC and so you will probably see more enzymes when you run this.
AP remap
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
CL -notran -sbeg 1 -send 60
IN tembl:j01636
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.remap
FZ = 1850
FP /^\s+Hin6I\s+2\s+HinP1I,HspAI\n/
//

ID remap-ex3
UC This is an example where all enzymes in the REBASE database are used
UC but the -limit qualifier is not set so that all of the enzymes are
UC displayed and not just only the prototypes of the isoschizomers.
UC This is run with a small test version of the restriction enzyme database
UC and so you will probably see more enzymes when you run this.
AP remap
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
CL -notran -sbeg 1 -send 60 -nolimit
IN tembl:j01636
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.remap
FZ = 2412
FP /^\s+TaqI\s+1\s+\n/
//

ID remap-ex4
UC This shows the 'flat' format:
UC This is run with a small test version of the restriction enzyme database
UC and so you will probably see more enzymes when you run this.
AP remap
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
CL -notran -sbeg 1 -send 60 -flat
IN tembl:j01636
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.remap
FZ = 2243
FP /^\s+Hin6I\s+2\s+HinP1I,HspAI\n/
//

ID restover-ex
AP restover
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
IN tembl:x65923
IN cg
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.restover
FZ = 1123
FP /^# Number of hits with any overlap: 54\n/
FP /^\s+11\s+TaqI\s+TCGA\s+11\s+13\s+\n/
//

ID restrict-ex
AP restrict
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
IN tembl:x65923
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.restrict
FP /^\s+11\s+14\s+[+]\s+TaqI\s+TCGA\s+11\s+13\s+\.\s+\.\s+\.\s+\.\s+\.\s+\.\n/
FP /^\s+125\s+135\s+[+]\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+\.\s+\.\s+148\s+143\s+\.\s+\.\n/
//

ID restrict-ex2
UC This gives the lengths of the restriction fragments produced by
UC cutting with all of the specified enzymes.
AP restrict
CL -fragments
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
IN tembl:x65923
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.restrict
FP /^\s+11\s+14\s+[+]\s+TaqI\s+TCGA\s+11\s+13\s+11\s+14\s+\.\s+\.\s+\.\s+\.\n/
FP /^\s+125\s+135\s+[+]\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+3\s+12\s+148\s+143\s+20\s+3\n/
FP /^#\s+79/
//

ID restrict-ex3
UC This gives the lengths of the restriction fragments created by
UC cutting with just one of each of the specified enzymes in turn.
AP restrict
CL -solofragment
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
IN tembl:x65923
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.restrict
FP /^\s+11\s+14\s+[+]\s+TaqI\s+TCGA\s+11\s+13\s+11\s+83\s+\.\s+\.\s+\.\s+\.\n/
FP /^\s+125\s+135\s+[+]\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+116\s+32\s+148\s+143\s+32\s+370\n/
FP /^#\s+3\s+13\s+25\s+33\s+37\s+114/
//

ID restrict-nonpal
UC Tests non-palindromic sites
AP restrict
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
CL -enzymes BseYI
IN asis:GCTGGGTTTCCCAGC 
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI asis.restrict
FP /^\s+1\s+6\s+[-]\s+BseYI\s+CCCAGC\s+1\s+5\s+\.\s+\.\s+\.\s+\.\s+\.\s+\.\n/
FP /^\s+10\s+15\s+[+]\s+BseYI\s+\CCCAGC\s+10\s+14\s+\.\s+\.\s+\.\s+\.\s+\.\s+\.\n/
//

ID revseq-ex
UC To create the reverse complement (reverse sense) of 'tembl:x65923' in the file 'x65923.rev':
AP revseq
CL tembl:x65923 x65923.rev
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.rev
FZ = 573
FP /^>X65923 X65923\.1 Reversed: H\.sapiens fau mRNA\n/
FP /^gtcccagctaccgcgaagatggagtcgagaaagaggaa\n/
//

ID revseq-ex2
UC To create the complement of 'tembl:x65923' in the file 'x65923.rev':
AP revseq
CL tembl:x65923 x65923.rev -norev
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.rev
FZ = 563
FP /^agattattttttcggtgaatcaagtcagtttttttttt\n/
//

ID revseq-ex3
UC To create the reverse of 'tembl:x65923' in the file 'x65923.rev':
AP revseq
CL tembl:x65923 x65923.rev -nocomp
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.rev
FZ = 563
FP /^cagggtcgatggcgcttctacctcagctctttctcctt\n/
//

ID seealso-ex
AP seealso
IN matcher
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 11
FP /^seqmatchall/
FP /^supermatcher/
FP /^water/
FP /^wordfinder/
FP /^wordmatch/
//

ID seqcount-ex
AP seqcount
CL "tembl:*" -out tembl.seqcount
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI tembl.seqcount
FC = 1
FP /^53\n/
//

ID seqmatchall-ex
UC Here is an example using an increased word size to avoid accidental matches:
AP seqmatchall
IN @../../data/eclac.list
IN 15
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.seqmatchall
FZ = 1623
FP /^  1832 J01636 +[+] +5646\.\.7477     X51872 +[+] +1\.\.1832\n/
FP /^  1113 J01636 +[+] +49\.\.1161     V00294 +[+] +1\.\.1113\n/
FP /^  1500 J01636 +[+] +4305\.\.5804     V00295 +[+] +1\.\.1500\n/
FP /^  3078 J01636 +[+] +1287\.\.4364     V00296 +[+] +1\.\.3078\n/
FP /^   159 X51872 +[+] +1\.\.159      V00295 +[+] +1342\.\.1500\n/
FP /^    60 V00295 +[+] +1\.\.60       V00296 +[+] +3019\.\.3078\n/
//

###########################################################################

# first entry in first file
ID seqret-dbidfilefirst
AP seqret
CL -auto tembl:H45989 test.out
FI test.out
FP 1 /\A>H45989 /
//

# last entry in last file
ID seqret-dbidfilelast
AP seqret
CL -auto tembl-id:U23808 test.out
FI test.out
FP 1 /\A>U23808 /
//

# last entry in last file
ID seqret-dbacfilelast
AP seqret
CL -auto tembl-acc:U23808 test.out
FI test.out
FP 1 /\A>U23808 U23808\.2 /
//

ID seqret-dbacfirst
AP seqret
CL -auto tembl-acc:AB000095 test.out
FI test.out
FP 1 /\A>AB000095 AB000095\.1 /
//

ID seqret-dbacnextlast
AP seqret
CL -auto tembl-acc:Z52466 test.out
FI test.out
FP 1 /\A>Z52466 Z52466\.1 /
//

ID seqret-dbaclast
AP seqret
CL -auto tembl-acc:Z69719 test.out
FI test.out
FP 1 /\A>Z69719 Z69719\.1 /
//

##########################################################################
#
# sequence input formats ... specified with -sformat and as -inauto
#                            also preferably as -inmulti
#                            where FASTA can check handling of various IDs
#                            could test with infoseq for length/id/acc/org
#
# todo:
#   swiss (sw swissprot)
#   pdb
#   pdbseq
#   pbdnuc
#   pdbnucseq
#   gifasta
#   pearson
#   fastq
#   fastq-sanger
#   fastq-solexa
#   fastq-illumina
#   sam
#   refseq
#   refseqp
#   genpept
#   ace
#   consed
#   dbid
#   hennig86
#   jackknifer
#   nexus (paup)
#   treecon
#   mega
#   igstrict
#   ig (no auto detect)
#   asis
#   gff2
#   gff3
#   biomart
#   bam
#   ensembl
#   das
#   
# also various fasta ids (test what ID is returned)
#
#
# also output formats (similar list)
#
# also seq+feature for thse which support features
# also nuc+prot if appropriate
#
# also sets of sets (phylip etc.) is multiset.
#
# script to process entrails output, check test names.
#
##########################################################################

ID seq-inlist-good
AP seqret
CL -auto @../../data/good.list test.out -osf swiss
FI test.out
FZ = 599
FP 3 /^ID   .* AA\.\n/
FP /^SQ   SEQUENCE   56 AA;  6465 MW;  48CB2E252357CBF6 CRC64;/
//

ID seq-inlist-bad
AP seqret
CL -auto @../../data/bad.list test.out -osf swiss
FI stderr
FZ = 112
FP 0 /Warning: /
FP 2 /Error: /
FP 0 /Died: /
FP /^Error: Failed to open filename '\.\.\/\.\.\/data\/alignc\.prot'\n/
FP /^Error: Failed to read sequence '\.\.\/\.\.\/data\/alignc\.prot'\n/
FI test.out
FP 3 /^ID   .* AA\.\n/
FP /^SQ   SEQUENCE   56 AA;  6465 MW;  48CB2E252357CBF6 CRC64;/
//

ID seq-inlist-ugly
AP seqret
CL -auto @../../data/ugly.list test.out -osf embl
FI stderr
FZ = 47
FP /^Error: Failed to read sequence 'tembl:V002944'\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FI test.out
FP 2 /^ID   .* BP\.\n/
FP /^SQ   Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/
//

ID seq-inlist-uglyfirst
AP seqret
CL -auto @../../data/uglyfirst.list test.out -osf embl
FI stderr
FZ = 47
FP /^Error: Failed to read sequence 'tembl:V002944'\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FI test.out
FP 2 /^ID   .* BP\.\n/
FP /^SQ   Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/
//

ID seq-inlist-uglylast
AP seqret
CL -auto @../../data/uglylast.list test.out -osf embl
FI stderr
FZ = 47
FP /^Error: Failed to read sequence 'tembl:V002944'\n/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FI test.out
FP 2 /^ID   .* BP\.\n/
FP /^SQ   Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/
//

ID seq-inlist-uglyall
AP seqret
CL -auto @../../data/uglyall.list test.out -osf embl
FI stderr
FZ = 141
FP /^Error: Failed to read sequence 'tembl:V002943'\n/
FP /^Error: Failed to read sequence 'tembl:V002944'\n/
FP /^Error: Failed to read sequence 'tembl:V002945'\n/
FP 0 /Warning: /
FP 3 /Error: /
FP 0 /Died: /
FI test.out
FP 2 /^ID   .* BP\.\n/
FP /^SQ   Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/
//

ID seq-inlist-testdb
AP seqret
CL -auto @../../data/testdb.list test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/
FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/
FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/
FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/
//

ID seq-inlist-testdb-sbegin
AP seqret
CL -auto @../../data/testdb.list -sbegin 11 test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/
FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/
FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/
FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/
//

ID seq-inlist-testdb-send
AP seqret
CL -auto @../../data/testdb.list -send -11 test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/
FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/
FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/
FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/
//

ID seq-inlist-testdb-strim
AP seqret
CL -auto @../../data/testdb.list -sbegin 11 -send -11 test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/
FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/
FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/
FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/
//

ID seq-inlist-testdb-strimrev
AP seqret
CL -auto @../../data/testdb.list -sbegin 11 -send -11 -srev test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nTTTTGGGGCCCAAATTGGCAGTAACCGGGTTTAAAACCCC\n/
FP />TCGAseq [^\n]+\nAAAAGGGGCCCTTTAAGGCTGATTCCGGGAAATTTTCCCC\n/
FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/
FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/
//

ID seq-set-inlist-testdb
AQ seqretset
CL -auto @../../data/testdb.list test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/
FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/
FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/
FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/
//

ID seq-set-inlist-testdb-sbegin
AQ seqretset
CL -auto @../../data/testdb.list -sbegin 11 test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/
FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/
FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/
FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/
//

ID seq-set-inlist-testdb-send
AQ seqretset
CL -auto @../../data/testdb.list -send -11 test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/
FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/
FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/
FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/
//

ID seq-set-inlist-testdb-strim
AQ seqretset
CL -auto @../../data/testdb.list -sbegin 11 -send -11 test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/
FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/
FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/
FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/
//

ID seq-set-inlist-testdb-strimrev
AQ seqretset
CL -auto @../../data/testdb.list -sbegin 11 -send -11 -srev test.out -osf fasta
FI test.out
FP 4 /^>/
FP />ACGTseq [^\n]+\nTTTTGGGGCCCAAATTGGCAGTAACCGGGTTTAAAACCCC\n/
FP />TCGAseq [^\n]+\nAAAAGGGGCCCTTTAAGGCTGATTCCGGGAAATTTTCCCC\n/
FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/
FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/
//

ID seq-inauto-acedb
AP seqret
CL -auto ../../data/dna.acedb test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-acedb
AP seqret
CL -auto acedb::../../data/dna.acedb test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-acedb
AP seqret
CL -auto ../../data/dna.acedb -sf acedb test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-codata
AP seqret
CL -auto ../../data/dna.codata test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-codata
AP seqret
CL -auto codata::../../data/dna.codata test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-codata
AP seqret
CL -auto ../../data/dna.codata -sf codata test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-embl
AP seqret
CL -auto ../../data/dna.embl test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-embl
AP seqret
CL -auto embl::../../data/dna.embl test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-embl
AP seqret
CL -auto ../../data/dna.embl -sf embl test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-em
AP seqret
CL -auto ../../data/dna.embl -sf em test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-experiment
AP seqret
CL -auto ../../data/xb63c7.s1.exp test.out -osf embl
FI test.out
FP /^ID   .* 439 BP\.\n/
FP /^SQ   Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/
//

ID seq-inusa-experiment
AP seqret
CL -auto experiment::../../data/xb63c7.s1.exp test.out -osf embl
FI test.out
FP /^ID   .* 439 BP\.\n/
FP /^SQ   Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/
//

ID seq-in-experiment
AP seqret
CL -auto ../../data/xb63c7.s1.exp -sf experiment test.out -osf embl
FI test.out
FP /^ID   .* 439 BP\.\n/
FP /^SQ   Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/
//

ID seq-inauto-fasta
AP seqret
CL -auto ../../data/dna.fasta test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-fasta
AP seqret
CL -auto fasta::../../data/dna.fasta test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-fasta
AP seqret
CL -auto ../../data/dna.fasta -sf fasta test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-innuc-fasta
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/dna.fasta -snuc -sf fasta -outfile test.out
FI test.out
FC = 2
FP /^fasta::\S+\t-\tFASTA\tF10002\tN\t100\t/
//

ID seq-inprot-fasta
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/prot.fasta -sprot -sf fasta -outfile test.out
FI test.out
FC = 2
FP /^fasta::\S+\t-\tFASTA\tF00001\tP\t100\t/
//

ID seq-in-fastq
AP seqret
CL -auto ../../data/fastqall.sanger -sf fastq test.out -osf experiment
FI test.out
FC = 5
FP /^ID   .* 94 BP\.\n/
FP /^SQ   Sequence 94 BP; 24 A; 24 C; 23 G; 23 T; 0 other;/
//

ID seq-inauto-fastq
AP seqret
CL -auto ../../data/fastqall.sanger test.out -osf experiment
FI test.out
FC = 5
FP /^ID   .* 94 BP\.\n/
FP /^SQ   Sequence 94 BP; 24 A; 24 C; 23 G; 23 T; 0 other;/
//

ID seq-in-fastq-illumina
AP seqret
CL -auto ../../data/fastqall.illumina13 -sf fastq-illumina test.out -osf experiment
FI test.out
FC = 7
FP /^ID   .* 41 BP\.\n/
FP /^AV   20 19 18 17 16 15 14 13 12 11 10  9  8  7  6  5  4  3  2  1\n/
FP /^SQ   Sequence 41 BP; 11 A; 10 C; 10 G; 10 T; 0 other;\n/
//

ID seq-in-fastq-sanger
AP seqret
CL -auto ../../data/fastqall.sanger -sf fastq-sanger test.out -osf experiment
FI test.out
FC = 10
FP /^ID   .* 94 BP\.\n/
FP /^AV   73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 55 54\n/
FP /^SQ   Sequence 94 BP; 24 A; 24 C; 23 G; 23 T; 0 other;\n/
//

ID seq-in-fastq-solexa
AP seqret
CL -auto ../../data/fastqall.solexa -sf fastq-solexa test.out -osf experiment
FI test.out
FC = 7
FP /^ID   .* 46 BP\.\n/
FP /^AV   20 19 18 17 16 15 14 13 12 11 10  9  8  7  6  6  5  4  4  3\n/
FP /^SQ   Sequence 46 BP; 12 A; 12 C; 11 G; 11 T; 0 other;\n/
//

ID seq-inauto-gcg
AP seqret
CL -auto ../../data/dna.gcg test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-gcg
AP seqret
CL -auto gcg::../../data/dna.gcg test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-gcg
AP seqret
CL -auto ../../data/dna.gcg -sf gcg test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-innuc-gcg
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/dna.gcg -snuc -sf gcg -outfile test.out
FI test.out
FC = 2
FP /^gcg::\S+\t-\tGCG\t-\tN\t100\t/
//

ID seq-inprot-gcg
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/prot.gcg -sf gcg -outfile test.out
FI test.out
FC = 2
FP /^gcg::\S+\t-\tGCG\t-\tP\t100\t/
//

ID seq-inauto-gcg8
AP seqret
CL -auto ../../data/dna.gcg8 test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-gcg8
AP seqret
CL -auto gcg8::../../data/dna.gcg8 test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-gcg8
AP seqret
CL -auto ../../data/dna.gcg8 -sf gcg8 test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-genbank
AP seqret
CL -auto ../../data/dna.genbank test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-genbank
AP seqret
CL -auto genbank::../../data/dna.genbank test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-genbank
AP seqret
CL -auto ../../data/dna.genbank -sf genbank test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-gb
AP seqret
CL -auto ../../data/dna.genbank -sf gb test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-ddbj
AP seqret
CL -auto ../../data/dna.genbank -sf ddbj test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-genpept
AP seqret
CL -auto ../../data/acn78416.genpept -sf genpept test.out -osf swiss
CC reference number and range only, no details parsed
FI test.out
FC = 28
FP 2 /^RN   /
FP /^ID   .* 225 AA\.\n/
FP /^DT   21-MAR-2009, entry version 1.\n/
FP /^SQ   SEQUENCE   225 AA;  25874 MW;  EDD076FAC2CFFD74 CRC64;\n/
//

ID seq-in-gifasta
AP seqret
CL -auto ../../data/ncbi.gifasta -sf gifasta test.out -osf swiss
FI test.out
FP /^ID   .* 8 AA\.\n/
FP /^SQ   SEQUENCE   8 AA;  950 MW;  61E059CB04176058 CRC64;/
//

ID seq-innuc-gifasta
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/ncbinuc.gifasta -snuc -sf gifasta -outfile test.out
FI test.out
FC = 2
FP /^gifasta::\S+\t-\t123456\t-\tN\t8\t/
//

ID seq-inprot-gifasta
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/ncbi.gifasta -sprot -sf gifasta -outfile test.out
FI test.out
FC = 2
FP /^gifasta::\S+\t-\t123456\t-\tP\t8\t/
//

ID seq-inauto-ig
AP seqret
CL -auto ../../data/dna.ig test.out -osf embl
FI test.out
FP /^ID   .* 100 BP/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-ig
AP seqret
CL -auto ig::../../data/dna.ig test.out -osf embl
FI test.out
FP /^ID   .* 100 BP/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-ig
AP seqret
CL -auto ../../data/dna.ig -sf ig test.out -osf embl
FI test.out
FP /^ID   .* 100 BP/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-ncbi
AP seqret
CL -auto ../../data/dna.ncbi test.out -osf embl
FI test.out
FP /^ID   .* 100 BP/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-ncbi
AP seqret
CL -auto ncbi::../../data/dna.ncbi test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-ncbi
AP seqret
CL -auto ../../data/dna.ncbi -sf ncbi test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-nbrf
AP seqret
CL -auto ../../data/prot.nbrf test.out -osf swiss
FI test.out
FZ = 251
FP /^ID   pir .* 90 AA\.\n/
FP /^DE   example pir format\n/
FP /^SQ   SEQUENCE   90 AA;  9685 MW;  5B548D9C397EC1FE CRC64;/
//

ID seq-inusa-nbrf
AP seqret
CL -auto nbrf::../../data/prot.nbrf test.out -osf swiss
FI test.out
FZ = 251
FP /^ID   pir .* 90 AA\.\n/
FP /^DE   example pir format\n/
FP /^SQ   SEQUENCE   90 AA;  9685 MW;  5B548D9C397EC1FE CRC64;/
//

ID seq-in-nbrf
AP seqret
CL -auto ../../data/prot.nbrf -sf nbrf test.out -osf swiss
FI test.out
FZ = 251
FP /^ID   pir .* 90 AA\.\n/
FP /^DE   example pir format\n/
FP /^SQ   SEQUENCE   90 AA;  9685 MW;  5B548D9C397EC1FE CRC64;/
//

ID seq-innuc-nbrf
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/dna.nbrf -snuc -sf nbrf -outfile test.out
FI test.out
FC = 2
FP /^nbrf::\S+\t-\tGENBANK\t-\tN\t100\t/
//

ID seq-inprot-nbrf
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/prot.nbrf -sprot -sf nbrf -outfile test.out
FI test.out
FC = 2
FP /^nbrf::\S+\t-\tpir\t-\tP\t90\t/
//

ID seq-in-pir
AP seqret
CL -auto ../../data/prot.nbrf -sf pir test.out -osf swiss
FI test.out
FZ = 251
FP /^ID   pir .* 90 AA\.\n/
FP /^DE   example pir format\n/
FP /^SQ   SEQUENCE   90 AA;  9685 MW;  5B548D9C397EC1FE CRC64;/
//

ID seq-inauto-nexus
AP seqret
CL -auto ../../data/protalign.nxs test.out -osf swiss
FI test.out
FP /^ID   .* 272 AA/
FP /^SQ   SEQUENCE   272 AA;  28915 MW;  C35D30BD3F2C74AC CRC64;\n/
FP /^SQ   SEQUENCE   272 AA;  29902 MW;  4A50E6FE63CE4ED5 CRC64;\n/
//

ID seq-inusa-nexus
AP seqret
CL -auto nexus::../../data/protalign.nxs test.out -osf swiss
FI test.out
FP /^ID   .* 272 AA/
FP /^SQ   SEQUENCE   272 AA;  28915 MW;  C35D30BD3F2C74AC CRC64;\n/
FP /^SQ   SEQUENCE   272 AA;  29902 MW;  4A50E6FE63CE4ED5 CRC64;\n/
//

ID seq-in-nexus
AP seqret
CL -auto ../../data/protalign.nxs -sf nexus test.out -osf swiss
FI test.out
FP /^ID   .* 272 AA/
FP /^SQ   SEQUENCE   272 AA;  28915 MW;  C35D30BD3F2C74AC CRC64;\n/
FP /^SQ   SEQUENCE   272 AA;  29902 MW;  4A50E6FE63CE4ED5 CRC64;\n/
//

ID seq-in-pdb
AP seqret
CL -auto ../../data/1tos.pdb -sf pdb test.out -osf swiss
CC PDB format reads all 3 models
FI test.out
FZ = 396
FP /^ID   1TOS_A1 .* 10 AA\.\n/
FP 3 /^ID   1TOS_A\d .* 10 AA\.\n/
FP /^SQ   SEQUENCE   10 AA;  1063 MW;  316593786B5AADC7 CRC64;/
//

ID seq-in-pdbnuc
AP seqret
CL -auto ../../data/133d.pdb -sf pdbnuc test.out -osf embl
CC PDBNUC format reads single seqres
FI test.out
FZ = 390
FP 2 /^ID   133D_[A-Z]; .* 5 BP\.\n/
FP 1 /^ID   133D_A; .* 5 BP\.\n/
FP /^SQ   Sequence 5 BP; 0 A; 2 C; 3 G; 0 T; 0 other;/
//

ID seq-in-pdbnucseq
AP seqret
CL -auto ../../data/133d.pdb -sf pdbnucseq test.out -osf embl
CC PDBNUC format reads single seqres
FI test.out
FZ = 390
FP 2 /^ID   133D_[A-Z]; .* 5 BP\.\n/
FP 1 /^ID   133D_A; .* 5 BP\.\n/
FP /^SQ   Sequence 5 BP; 0 A; 2 C; 3 G; 0 T; 0 other;/
//

ID seq-in-pdbseq
AP seqret
CL -auto ../../data/1tos.pdb -sf pdbseq test.out -osf swiss
CC PDBSEQ format reads single seqres
FI test.out
FZ = 132
FP /^ID   1TOS_A .* 10 AA\.\n/
FP 1 /^ID   1TOS_A.* 10 AA\.\n/
FP /^SQ   SEQUENCE   10 AA;  1063 MW;  316593786B5AADC7 CRC64;/
//

ID seq-inauto-pdb
AP seqret
CL -auto ../../data/1tos.pdb test.out -osf swiss
CC PDB format reads single seqres
FI test.out
FZ = 396
FP /^ID   1TOS_A1 .* 10 AA\.\n/
FP 3 /^ID   1TOS_A\d .* 10 AA\.\n/
FP /^SQ   SEQUENCE   10 AA;  1063 MW;  316593786B5AADC7 CRC64;/
//

ID seq-in-pearson
AP seqret
CL -auto ../../data/ncbi.gifasta -sf pearson test.out -osf swiss
FI test.out
FP /^ID   gi[\|]123456.* 8 AA\.\n/
FP /^SQ   SEQUENCE   8 AA;  950 MW;  61E059CB04176058 CRC64;/
//

ID seq-innuc-pearson
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/ncbinuc.gifasta -snuc -sf pearson -outfile test.out
FI test.out
FC = 2
FP /^pearson::\S+\t-\tgi\|123456\t-\tN\t8\t/
//

ID seq-inprot-pearson
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/ncbi.gifasta -sprot -sf pearson -outfile test.out
FI test.out
FC = 2
FP /^pearson::\S+\t-\tgi\|123456\t-\tP\t8\t/
//

ID seq-inauto-raw
AP seqret
CL -auto ../../data/dna.text test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-raw
AP seqret
CL -auto raw::../../data/dna.text test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-raw
AP seqret
CL -auto ../../data/dna.text -sf raw test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-refseq
AP seqret
CL -auto ../../data/pao-short.refseq -sf refseq test.out -osf embl
FI test.out
FP /^ID   .* 7004 BP\.\n/
FP /^SQ   Sequence 7004 BP; 1431 A; 2216 C; 2102 G; 1255 T; 0 other;/
//

ID seq-in-refseq-genbank
AP seqret
CL -auto ../../data/pao-short.refseq -sf genbank test.out -osf embl
FI test.out
FP /^ID   .* 7004 BP\.\n/
FP /^SQ   Sequence 7004 BP; 1431 A; 2216 C; 2102 G; 1255 T; 0 other;/
//

ID seq-in-refseqp
AP seqret
CL -auto ../../data/protein.refseqp -sf refseqp test.out -osf swiss
CC reference number and range only, no details parsed
FI test.out
FC = 87
FP 10 /^RP   1-182$/
FP 10 /^RP   /
FP 10 /^RL   /
FP 6 /^CC   /
FP /^ID   .* 182 AA\.\n/
FP /^SQ   SEQUENCE   182 AA;  22127 MW;  C7B1D95FB43A4A3F CRC64;\n/
//

ID seq-in-sam
AP seqret
CL -auto ../../data/xxx.sam -sf sam test.out -osf embl
FI test.out
FP /^ID   read_28833_29006_6945;.* 35 BP\.\n/
FP 2 /^ID   /
FP /^SQ   Sequence 35 BP; 6 A; 9 C; 8 G; 12 T; 0 other;\n/
//

ID seq-inauto-sam
AP seqret
CL -auto ../../data/xxx.sam test.out -osf embl
FI test.out
FP /^ID   read_28833_29006_6945;.* 35 BP\.\n/
FP 2 /^ID   /
FP /^SQ   Sequence 35 BP; 6 A; 9 C; 8 G; 12 T; 0 other;\n/
//

ID seq-innuc-sam
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/xxx.sam -sf sam -outfile test.out
FI test.out
FC = 3
FP /^sam::\S+\t-\tread_28833_29006_6945\t-\tN\t35\t48\.57/
FP /^sam::\S+\t-\tread_28701_28881_323b\t-\tN\t35\t57\.14/
//

ID seq-inauto-staden
AP seqret
CL -auto ../../data/dna.staden test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-staden
AP seqret
CL -auto staden::../../data/dna.staden test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-staden
AP seqret
CL -auto ../../data/dna.staden -sf staden test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-strider
AP seqret
CL -auto ../../data/dna.strider test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-strider
AP seqret
CL -auto strider::../../data/dna.strider test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-strider
AP seqret
CL -auto ../../data/dna.strider -sf strider test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-swiss
AP seqret
CL -auto ../../data/amir.swiss -sf swiss test.out -osf swiss
FI test.out
FP /^ID   AMIR_PSEAE .*Reviewed; *196 AA\.\n/
FP /^SQ   SEQUENCE   196 AA;  21903 MW;  306A4F30E8E4C6C0 CRC64;/
//

ID seq-in-sw
AP seqret
CL -auto ../../data/amir.swiss -sf sw test.out -osf swiss
FI test.out
FP /^ID   AMIR_PSEAE .*Reviewed; *196 AA\.\n/
FP /^SQ   SEQUENCE   196 AA;  21903 MW;  306A4F30E8E4C6C0 CRC64;/
//

ID seq-in-swissprot
AP seqret
CL -auto ../../data/amir.swiss -sf swissprot test.out -osf swiss
FI test.out
FP /^ID   AMIR_PSEAE .*Reviewed; *196 AA\.\n/
FP /^SQ   SEQUENCE   196 AA;  21903 MW;  306A4F30E8E4C6C0 CRC64;/
//

ID seq-inauto-swiss
AP seqret
CL -auto ../../data/amir.swiss test.out -osf swiss
FI test.out
FP /^ID   AMIR_PSEAE .*Reviewed; *196 AA\.\n/
FP /^SQ   SEQUENCE   196 AA;  21903 MW;  306A4F30E8E4C6C0 CRC64;/
//

ID seq-inauto-textonly
AP seqret
CL -auto ../../data/dna.text test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inusa-textonly
AP seqret
CL -auto textonly::../../data/dna.text test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-textonly
AP seqret
CL -auto ../../data/dna.text -sf textonly test.out -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-inauto-abi
AP seqret
CL -auto ../../data/abiview.abi test.out -osf embl
FI test.out
FZ = 1258
FP /^ID   .* 838 BP\.\n/
FP /^SQ   Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/
//

ID seq-inusa-abi
AP seqret
CL -auto abi::../../data/abiview.abi test.out -osf embl
FI test.out
FZ = 1258
FP /^ID   .* 838 BP\.\n/
FP /^SQ   Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/
//

ID seq-in-abi
AP seqret
CL -auto ../../data/abiview.abi -sf abi test.out -osf embl
FI test.out
FZ = 1258
FP /^ID   .* 838 BP\.\n/
FP /^SQ   Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/
//


ID seq-in-unknown
AP seqret
CL -auto ../../data/dna.text test.out -sf unknown -osf embl
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-innuc-unknown
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/dna.text -snuc -outfile test.out -sf unknown
FI test.out
FC = 2
FP /^raw::\S+\t-\t-\t-\tN\t100\t/
//

ID seq-inprot-unknown
AP infoseq
CL -nocolumn -delimiter "\t"
CL -auto ../../data/prot.text -sprot -outfile test.out -sf unknown
FI test.out
FC = 2
FP /^raw::\S+\t-\t-\t-\tP\t100\t/
//

ID seq-inusa-selex
AP seqret
CL -auto selex::../../data/test.selex test.out -osf embl
FI test.out
FZ = 587
FP 3 /^ID/
FP /^ID   lig28.* 31 BP\.\n/
FP /^SQ   Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/
//

ID seq-in-selex
AP seqret
CL -auto ../../data/test.selex -sf selex test.out -osf embl
FI test.out
FZ = 587
FP 3 /^ID/
FP /^ID   lig28.* 31 BP\.\n/
FP /^SQ   Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/
//

ID seq-inmultiauto-acedb
AP seqret
CL -auto ../../data/dna.m-acedb test.out -osf embl
FI test.out
FP 1 /^ID   ACEDBM1; .* 120 BP\.\n/
FP 1 /^ID   ACEDBM2; .* 120 BP\.\n/
FP 1 /^ID   ACEDBM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-acedb
AP seqret
CL -auto acedb::../../data/dna.m-acedb test.out -osf embl
FI test.out
FP 1 /^ID   ACEDBM1; .* 120 BP\.\n/
FP 1 /^ID   ACEDBM2; .* 120 BP\.\n/
FP 1 /^ID   ACEDBM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-acedb
AP seqret
CL -auto ../../data/dna.m-acedb -sf acedb test.out -osf embl
FI test.out
FP 1 /^ID   ACEDBM1; .* 120 BP\.\n/
FP 1 /^ID   ACEDBM2; .* 120 BP\.\n/
FP 1 /^ID   ACEDBM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-in-clustal
AP seqret
CL -auto ../../data/globins.m-aln -sf clustal test.out -osf swiss
FI test.out
FP 1 /^ID   HBB_HUMAN  .* 167 AA\.\n/
FP 1 /^ID   HBA_HUMAN  .* 167 AA\.\n/
FP 7 /^ID   /
FP 7 /^SQ   SEQUENCE   \d+ AA;  \d+ MW;  \S+ CRC64;\n/
FP 1 /^SQ   SEQUENCE   167 AA;  15867 MW;  BEAE9EB4529C39C3 CRC64;\n/
//

ID seq-inauto-clustal
AP seqret
CL -auto ../../data/globins.m-aln test.out -osf swiss
FI test.out
FP 1 /^ID   HBB_HUMAN  .* 167 AA\.\n/
FP 1 /^ID   HBA_HUMAN  .* 167 AA\.\n/
FP 7 /^ID   /
FP 7 /^SQ   SEQUENCE   \d+ AA;  \d+ MW;  \S+ CRC64;\n/
FP 1 /^SQ   SEQUENCE   167 AA;  15867 MW;  BEAE9EB4529C39C3 CRC64;\n/
//

ID seq-in-aln
AP seqret
CL -auto ../../data/globins.m-aln -sf aln test.out -osf swiss
FI test.out
FP 1 /^ID   HBB_HUMAN  .* 167 AA\.\n/
FP 1 /^ID   HBA_HUMAN  .* 167 AA\.\n/
FP 7 /^ID   /
FP 7 /^SQ   SEQUENCE   \d+ AA;  \d+ MW;  \S+ CRC64;\n/
FP 1 /^SQ   SEQUENCE   167 AA;  15867 MW;  BEAE9EB4529C39C3 CRC64;\n/
//

ID seq-inmultiauto-aln
AP seqret
CL -auto ../../data/globins.m-aln test.out -osf swiss
FI test.out
FP 1 /^ID   HBB_HUMAN  .* 167 AA\.\n/
FP 1 /^ID   HBA_HUMAN  .* 167 AA\.\n/
FP 7 /^ID   /
FP 7 /^SQ   SEQUENCE   \d+ AA;  \d+ MW;  \S+ CRC64;\n/
FP 1 /^SQ   SEQUENCE   167 AA;  15867 MW;  BEAE9EB4529C39C3 CRC64;\n/
//

ID seq-inmultiusa-aln
AP seqret
CL -auto aln::../../data/globins.m-aln test.out -osf swiss
FI test.out
FP 1 /^ID   HBB_HUMAN  .* 167 AA\.\n/
FP 1 /^ID   HBA_HUMAN  .* 167 AA\.\n/
FP 7 /^ID   /
FP 7 /^SQ   SEQUENCE   \d+ AA;  \d+ MW;  \S+ CRC64;\n/
FP 1 /^SQ   SEQUENCE   167 AA;  15867 MW;  BEAE9EB4529C39C3 CRC64;\n/
//

ID seq-inmulti-aln
AP seqret
CL -auto ../../data/globins.m-aln  -sf aln test.out -osf swiss
FI test.out
FP 1 /^ID   HBB_HUMAN  .* 167 AA\.\n/
FP 1 /^ID   HBA_HUMAN  .* 167 AA\.\n/
FP 7 /^ID   /
FP 7 /^SQ   SEQUENCE   \d+ AA;  \d+ MW;  \S+ CRC64;\n/
FP 1 /^SQ   SEQUENCE   167 AA;  15867 MW;  BEAE9EB4529C39C3 CRC64;\n/
//

ID seq-inmultiauto-clustal
AP seqret
CL -auto ../../data/dna.m-clustal test.out -osf embl
FI test.out
FP 1 /^ID   ALNM1; .* 120 BP\.\n/
FP 1 /^ID   ALNM2; .* 120 BP\.\n/
FP 1 /^ID   ALNM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-clustal
AP seqret
CL -auto clustal::../../data/dna.m-clustal test.out -osf embl
FI test.out
FP 1 /^ID   ALNM1; .* 120 BP\.\n/
FP 1 /^ID   ALNM2; .* 120 BP\.\n/
FP 1 /^ID   ALNM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-clustal
AP seqret
CL -auto ../../data/dna.m-clustal -sf clustal test.out -osf embl
FI test.out
FP 1 /^ID   ALNM1; .* 120 BP\.\n/
FP 1 /^ID   ALNM2; .* 120 BP\.\n/
FP 1 /^ID   ALNM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-codata
AP seqret
CL -auto ../../data/dna.m-codata test.out -osf embl
FI test.out
FP 1 /^ID   C30001; .* 120 BP\.\n/
FP 1 /^ID   C30002; .* 120 BP\.\n/
FP 1 /^ID   C30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-codata
AP seqret
CL -auto codata::../../data/dna.m-codata test.out -osf embl
FI test.out
FP 1 /^ID   C30001; .* 120 BP\.\n/
FP 1 /^ID   C30002; .* 120 BP\.\n/
FP 1 /^ID   C30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-codata
AP seqret
CL -auto ../../data/dna.m-codata -sf codata test.out -osf embl
FI test.out
FP 1 /^ID   C30001; .* 120 BP\.\n/
FP 1 /^ID   C30002; .* 120 BP\.\n/
FP 1 /^ID   C30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-embl
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf embl
FI test.out
FP 1 /^ID   F30001; .* 120 BP\.\n/
FP 1 /^ID   F30002; .* 120 BP\.\n/
FP 1 /^ID   F30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-embl
AP seqret
CL -auto embl::../../data/dna.m-embl test.out -osf embl
FI test.out
FP 1 /^ID   F30001; .* 120 BP\.\n/
FP 1 /^ID   F30002; .* 120 BP\.\n/
FP 1 /^ID   F30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-embl
AP seqret
CL -auto ../../data/dna.m-embl -sf embl test.out -osf embl
FI test.out
FP 1 /^ID   F30001; .* 120 BP\.\n/
FP 1 /^ID   F30002; .* 120 BP\.\n/
FP 1 /^ID   F30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-fasta
AP seqret
CL -auto ../../data/dna.m-fasta test.out -osf embl
FI test.out
FP 1 /^ID   F30001; .* 120 BP\.\n/
FP 1 /^ID   F30002; .* 120 BP\.\n/
FP 1 /^ID   F30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-fasta
AP seqret
CL -auto fasta::../../data/dna.m-fasta test.out -osf embl
FI test.out
FP 1 /^ID   F30001; .* 120 BP\.\n/
FP 1 /^ID   F30002; .* 120 BP\.\n/
FP 1 /^ID   F30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-fasta
AP seqret
CL -auto ../../data/dna.m-fasta -sf fasta test.out -osf embl
FI test.out
FP 1 /^ID   F30001; .* 120 BP\.\n/
FP 1 /^ID   F30002; .* 120 BP\.\n/
FP 1 /^ID   F30003; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-fitch
AP seqret
CL -auto ../../data/dna.fitch test.out -osf embl
FI test.out
FP 1 /^ID   FASTAM1; .* 120 BP\.\n/
FP 1 /^ID   FASTAM2; .* 120 BP\.\n/
FP 1 /^ID   FASTAM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-fitch
AP seqret
CL -auto fitch::../../data/dna.fitch test.out -osf embl
FI test.out
FP 1 /^ID   FASTAM1; .* 120 BP\.\n/
FP 1 /^ID   FASTAM2; .* 120 BP\.\n/
FP 1 /^ID   FASTAM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-fitch
AP seqret
CL -auto ../../data/dna.fitch -sf fitch test.out -osf embl
FI test.out
FP 1 /^ID   FASTAM1; .* 120 BP\.\n/
FP 1 /^ID   FASTAM2; .* 120 BP\.\n/
FP 1 /^ID   FASTAM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-mase
AP seqret
CL -auto mase::../../data/test.mase test.out -osf swiss
FI test.out
FP 1 /^ID   Sequence1               Unreviewed;         120 AA\.\n/
FP 1 /^ID   Sequence2               Unreviewed;         120 AA\.\n/
FP 1 /^DE   First protein sequence\n/
FP 1 /^SQ   SEQUENCE   120 AA;  12728 MW;  F55A82D26A16578D CRC64;/
FP 2 /^ID/
//

ID seq-inmulti-mase
AP seqret
CL -auto ../../data/test.mase -sf mase test.out -osf swiss
FI test.out
FP 1 /^ID   Sequence1               Unreviewed;         120 AA\.\n/
FP 1 /^ID   Sequence2               Unreviewed;         120 AA\.\n/
FP 1 /^DE   First protein sequence\n/
FP 1 /^SQ   SEQUENCE   120 AA;  12728 MW;  F55A82D26A16578D CRC64;/
FP 2 /^ID/
//

ID seq-inmultiauto-msf
AP seqret
CL -auto ../../data/dna.msf test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-msf
AP seqret
CL -auto msf::../../data/dna.msf test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-msf
AP seqret
CL -auto ../../data/dna.msf -sf msf test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-msf8
AP seqret
CL -auto ../../data/dna.msf8 test.out -osf embl
FI test.out
FP 1 /^ID   fastam1; .* 121 BP\.\n/
FP 1 /^ID   fastam2; .* 121 BP\.\n/
FP 1 /^ID   fastam3; .* 121 BP\.\n/
FP 2 /^SQ   Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/
FP 1 /^SQ   Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/
//

ID seq-inmultiusa-msf8
AP seqret
CL -auto msf::../../data/dna.msf8 test.out -osf embl
FI test.out
FP 1 /^ID   fastam1; [^\n]* 121 BP\.\n/
FP 1 /^ID   fastam2; [^\n]* 121 BP\.\n/
FP 1 /^ID   fastam3; [^\n]* 121 BP\.\n/
FP 2 /^SQ   Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/
FP 1 /^SQ   Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/
//

ID seq-inmulti-msf8
AP seqret
CL -auto ../../data/dna.msf8 -sf msf test.out -osf embl
FI test.out
FP 1 /^ID   fastam1; .* 121 BP\.\n/
FP 1 /^ID   fastam2; .* 121 BP\.\n/
FP 1 /^ID   fastam3; .* 121 BP\.\n/
FP 2 /^SQ   Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/
FP 1 /^SQ   Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/
//

ID seq-inmultiauto-ncbi
AP seqret
CL -auto ../../data/dna.m-ncbi test.out -osf embl
FI test.out
FP 1 /^ID   N30001; .* 144 BP\.\n/
FP 1 /^ID   N30002; .* 144 BP\.\n/
FP 1 /^ID   N30003; .* 144 BP\.\n/
FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/
//

ID seq-inmultiusa-ncbi
AP seqret
CL -auto ncbi::../../data/dna.m-ncbi test.out -osf embl
FI test.out
FP 1 /^ID   N30001; .* 144 BP\.\n/
FP 1 /^ID   N30002; .* 144 BP\.\n/
FP 1 /^ID   N30003; .* 144 BP\.\n/
FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/
//

ID seq-inmulti-ncbi
AP seqret
CL -auto ../../data/dna.m-ncbi -sf ncbi test.out -osf embl
FI test.out
FP 1 /^ID   N30001; .* 144 BP\.\n/
FP 1 /^ID   N30002; .* 144 BP\.\n/
FP 1 /^ID   N30003; .* 144 BP\.\n/
FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/
//

ID seq-in-phylip
AP seqret
CL -auto ../../data/dna.phylip -sf phylip test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inauto-phylip
AP seqret
CL -auto ../../data/dna.phylip test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-phylip
AP seqret
CL -auto ../../data/dna.phylip test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-phylip
AP seqret
CL -auto phylip::../../data/dna.phylip test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-phylip
AP seqret
CL -auto ../../data/dna.phylip -sf phylip test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiauto-phylipnon
AP seqret
CL -auto ../../data/dna.phylip3 test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-phylipnon
AP seqret
CL -auto phylipnon::../../data/dna.phylip3 test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmulti-phylipnon
AP seqret
CL -auto ../../data/dna.phylip3 -sf phylipnon test.out -osf embl
FI test.out
FP 1 /^ID   MSFM1; .* 120 BP\.\n/
FP 1 /^ID   MSFM2; .* 120 BP\.\n/
FP 1 /^ID   MSFM3; .* 120 BP\.\n/
FP 2 /^SQ   Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/
FP 1 /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/
//

ID seq-inmultiusa-stockholm
AP seqret
CL -auto stockholm::../../data/PF00032_seed.sth test.out -osf swiss
FI test.out
FZ = 2304
FP 9 /^ID/
FP /^ID   PETD_SYNP2\/65-160       Reviewed;         116 AA\.\n/
FP /^SQ   SEQUENCE   116 AA;  12467 MW;  B077FB597F735C49 CRC64;/
//

ID seq-inmulti-stockholm
AP seqret
CL -auto ../../data/PF00032_seed.sth -sf stockholm test.out -osf swiss
FI test.out
FZ = 2304
FP 9 /^ID/
FP /^ID   PETD_SYNP2\/65-160       Reviewed;         116 AA\.\n/
FP /^SQ   SEQUENCE   116 AA;  12467 MW;  B077FB597F735C49 CRC64;/
//

ID seq-inmultiusa-stockholm2
AP seqret
CL -auto stockholm::../../data/PF00032_seed.pfam2 test.out -osf swiss
FI test.out
FZ = 2304
FP 9 /^ID/
FP /^ID   PETD_SYNP2\/65-160       Reviewed;         116 AA\.\n/
FP /^SQ   SEQUENCE   116 AA;  12467 MW;  B077FB597F735C49 CRC64;/
//

ID seq-inmulti-stockholm2
AP seqret
CL -auto ../../data/PF00032_seed.pfam2 -sf stockholm test.out -osf swiss
FI test.out
FZ = 2304
FP 9 /^ID/
FP /^ID   PETD_SYNP2\/65-160       Reviewed;         116 AA\.\n/
FP /^SQ   SEQUENCE   116 AA;  12467 MW;  B077FB597F735C49 CRC64;/
//

ID seq-inmultiusa-stockholm3
AP seqret
CL -auto stockholm::../../data/PF00032_seed.pfam3 test.out -osf swiss
FI test.out
FZ = 2304
FP 9 /^ID/
FP /^ID   PETD_SYNP2\/65-160       Reviewed;         116 AA\.\n/
FP /^SQ   SEQUENCE   116 AA;  12467 MW;  B077FB597F735C49 CRC64;/
//

ID seq-inmulti-stockholm3
AP seqret
CL -auto ../../data/PF00032_seed.pfam3 -sf stockholm test.out -osf swiss
FI test.out
FZ = 2304
FP 9 /^ID/
FP /^ID   PETD_SYNP2\/65-160       Reviewed;         116 AA\.\n/
FP /^SQ   SEQUENCE   116 AA;  12467 MW;  B077FB597F735C49 CRC64;/
//

ID seq-inmultiusa-stockholmdos
AP seqret
CL -auto stockholm::../../data/dosfile.sth test.out -osf swiss
FI test.out
FZ = 1234
FP 8 /^ID/
FP /^ID   YA80_HAEIN              Reviewed;          30 AA\.\n/
FP /^SQ   SEQUENCE   30 AA;  2175 MW;  3B8F297C2C1E4614 CRC64;/
//

ID seq-inmulti-stockholmdos
AP seqret
CL -auto ../../data/dosfile.sth -sf stockholm test.out -osf swiss
FI test.out
FZ = 1234
FP 8 /^ID/
FP /^ID   YA80_HAEIN              Reviewed;          30 AA\.\n/
FP /^SQ   SEQUENCE   30 AA;  2175 MW;  3B8F297C2C1E4614 CRC64;/
//

ID seq-inmultiauto-strider
AP seqret
CL -auto ../../data/dna.m-strider test.out -osf embl
FI test.out
FP 1 /^ID   STRIDERM1; .* 144 BP\.\n/
FP 1 /^ID   STRIDERM2; .* 144 BP\.\n/
FP 1 /^ID   STRIDERM3; .* 144 BP\.\n/
FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/
//

ID seq-inmultiusa-strider
AP seqret
CL -auto strider::../../data/dna.m-strider test.out -osf embl
FI test.out
FP 1 /^ID   STRIDERM1; .* 144 BP\.\n/
FP 1 /^ID   STRIDERM2; .* 144 BP\.\n/
FP 1 /^ID   STRIDERM3; .* 144 BP\.\n/
FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/
//

ID seq-inmulti-strider
AP seqret
CL -auto ../../data/dna.m-strider -sf strider test.out -osf embl
FI test.out
FP 1 /^ID   STRIDERM1; .* 144 BP\.\n/
FP 1 /^ID   STRIDERM2; .* 144 BP\.\n/
FP 1 /^ID   STRIDERM3; .* 144 BP\.\n/
FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/
//

ID seq-inauto-nonewline
AP seqret
CL -auto ../../data/dna.nonewline test.out -osf embl
FI test.out
FP /^ID   .* 48 BP\.\n/
FP /^SQ   Sequence 48 BP; 10 A; 10 C; 10 G; 10 T; 8 other;/
//

ID seq-inauto-empty
AP seqret
CL -auto stdin test.out -osf embl
ER 1
FI stderr
FZ = 109
FP /Error: Unable to read sequence 'stdin'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seq-in-badformat
##
## bad format name - but still reads (auto) it if it can
##
AP seqret
CL -auto ../../data/dna.fasta -sf badformat test.out -osf embl
FI stderr
FP /Unknown input format 'badformat'/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-in-badusaformat
##
## bad format name - but still reads (auto) it if it can
##
AP seqret
CL -auto badformat::../../data/dna.fasta test.out -osf embl
FI stderr
FP /Unknown input format 'badformat'/
FP 0 /Warning: /
FP 1 /Error: /
FP 0 /Died: /
FI test.out
FP /^ID   .* 100 BP\.\n/
FP /SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/
//

ID seq-outusa-acedb
AP seqret
CL -auto ../../data/dna.embl acedb::test.out
FI test.out
FZ = 116
FP /^DNA : "EMBL"\n/
//

ID seq-out-acedb
AP seqret
CL -auto ../../data/dna.embl test.out -osf acedb
FI test.out
FZ = 116
FP /^DNA : "EMBL"\n/
//

ID seq-outusa-asn1
AP seqret
CL -auto ../../data/dna.embl asn1::test.out
FI test.out
FZ = 291
FP /repr raw, mol dna, length 100, topology linear,/
FP /id \{ local id 1 \},/
//

ID seq-out-asn1
AP seqret
CL -auto ../../data/dna.embl test.out -osf asn1
FI test.out
FZ = 291
FP /repr raw, mol dna, length 100, topology linear,/
FP /id \{ local id 1 \},/
//

ID seq-outusa-codata
AP seqret
CL -auto ../../data/dna.embl codata::test.out
FI test.out
FZ = 419
FP /^     61 a c g t a c g t a c g t a c g t a c g t a c g t a c g t a c\n/
FP /^ENTRY           EMBL/
FP /^TITLE           EMBL FORMAT DNA SEQUENCE, 100 bases/
FP /^ACCESSION       E10002/
FP /^\/\/\/\n/
//

ID seq-out-codata
AP seqret
CL -auto ../../data/dna.embl test.out -osf codata
FI test.out
FZ = 419
FP /^     61 a c g t a c g t a c g t a c g t a c g t a c g t a c g t a c\n/
FP /^ENTRY           EMBL/
FP /^TITLE           EMBL FORMAT DNA SEQUENCE, 100 bases/
FP /^ACCESSION       E10002/
FP /^\/\/\/\n/
//

ID seq-outusa-debug
AP seqret
CL -auto ../../data/dna.embl debug::test.out
FI test.out
FZ = 1141
FP /^  Name: 'EMBL'\n/
FP /^  Accession: 'E10002'\n/
FP /^  SeqVersion: 'E10002\.34'\n/
FP /^  GenInfo Id: ''\n/
FP /^  Description: 'EMBL FORMAT DNA SEQUENCE'\n/
FP /^  Keywordlist: \(2\)\n/
FP /^    'DNA binding protein'\n/
FP /^    'repressor'\n/
FP /^  Taxonomy: 'Escherichia coli'\n/
FP /^  Taxlist: \(5\)\n/
FP /^    'Bacteria'\n/
FP /^    'Proteobacteria'\n/
FP /^    'gamma subdivision'\n/
FP /^    'Enterobacteriaceae'\n/
FP /^    'Escherichia'\n/
FP /^  Type: 'N'\n/
FP /^  Usa: 'debug::test\.out'\n/
FP /^  Input format: 'embl'\n/
FP /^  Ufo: ''\n/
FP /^  Entryname: 'EMBL'\n/
FP /^  File name: 'test\.out'\n/
FP /^  Extension: 'fasta'\n/
FP /^  Single: 'No'\n/
FP /^  Features: 'No'\n/
FP /^  Count: '0'\n/
FP /^  51  gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt  100\n/
//

ID seq-out-debug
AP seqret
CL -auto ../../data/dna.embl test.out -osf debug
FI test.out
FZ = 1134
FP /^  Name: 'EMBL'\n/
FP /^  Accession: 'E10002'\n/
FP /^  SeqVersion: 'E10002\.34'\n/
FP /^  GenInfo Id: ''\n/
FP /^  Description: 'EMBL FORMAT DNA SEQUENCE'\n/
FP /^  Keywordlist: \(2\)\n/
FP /^    'DNA binding protein'\n/
FP /^    'repressor'\n/
FP /^  Taxonomy: 'Escherichia coli'\n/
FP /^  Taxlist: \(5\)\n/
FP /^    'Bacteria'\n/
FP /^    'Proteobacteria'\n/
FP /^    'gamma subdivision'\n/
FP /^    'Enterobacteriaceae'\n/
FP /^    'Escherichia'\n/
FP /^  Type: 'N'\n/
FP /^  Usa: 'test\.out'\n/
FP /^  Input format: 'embl'\n/
FP /^  Ufo: ''\n/
FP /^  Entryname: 'EMBL'\n/
FP /^  File name: 'test\.out'\n/
FP /^  Extension: 'debug'\n/
FP /^  Single: 'No'\n/
FP /^  Features: 'No'\n/
FP /^  Count: '0'\n/
FP /^  51  gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt  100\n/
//

ID seq-outusa-embl
AP seqret
CL -auto ../../data/dna.embl embl::test.out
FI test.out
FZ = 487
FP /^ID   E10002; SV 34; linear; unassigned DNA; STD; UNC; 100 BP\.\n/
FP /^AC   E10002;\n/
FP /^DE   EMBL FORMAT DNA SEQUENCE\n/
FP /^KW   DNA binding protein; repressor\.\n/
FP /^OS   Escherichia coli\n/
FP /^OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/
FP /^OC   Escherichia\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/
FP /^     acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt        60\n/
//

ID seq-out-embl
AP seqret
CL -auto ../../data/dna.embl test.out -osf embl
FI test.out
FZ = 487
FP /^ID   E10002; SV 34; linear; unassigned DNA; STD; UNC; 100 BP\.\n/
FP /^AC   E10002;\n/
FP /^DE   EMBL FORMAT DNA SEQUENCE\n/
FP /^KW   DNA binding protein; repressor\.\n/
FP /^OS   Escherichia coli\n/
FP /^OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/
FP /^OC   Escherichia\.\n/
FP /^SQ   Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/
FP /^     acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt        60\n/
//

ID seq-outusa-experiment
AP seqret
CL -auto ../../data/dna.embl experiment::test.out
FI test.out
FZ = 469
FP /^ID   EMBL       standard; DNA; UNC; 100 BP\.\n/
FP /^\s+ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\s+100\n/
//

ID seq-out-experiment
AP seqret
CL -auto ../../data/dna.embl test.out -osf experiment
FI test.out
FZ = 469
FP /^ID   EMBL       standard; DNA; UNC; 100 BP\.\n/
FP /^\s+ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\s+100\n/
//

ID seq-outusa-fasta
AP seqret
CL -auto ../../data/dna.embl fasta::test.out
FI test.out
FZ = 143
FP /^>EMBL E10002\.34 EMBL FORMAT DNA SEQUENCE\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-out-fasta
AP seqret
CL -auto ../../data/dna.embl test.out -osf fasta
FI test.out
FZ = 143
FP /^>EMBL E10002\.34 EMBL FORMAT DNA SEQUENCE\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-outusa-fitch
AP seqret
CL -auto ../../data/dna.embl fitch::test.out
FI test.out
FZ = 152
FP /^EMBL, 100 bases\n/
FP /^ acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt\n/
//

ID seq-out-fitch
AP seqret
CL -auto ../../data/dna.embl test.out -osf fitch
FI test.out
FZ = 152
FP /^EMBL, 100 bases\n/
FP /^ acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt\n/
//

ID seq-outusa-gcg
AP seqret
CL -auto ../../data/dna.embl gcg::test.out
FI test.out
FZ = 211
FP /^\!\!NA_SEQUENCE 1\.0\n/
FP /^EMBL  Length: 100  Type: N  Check: 6856 \.\.\n/
FP /^   1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac\n/
//

ID seq-out-gcg
AP seqret
CL -auto ../../data/dna.embl test.out -osf gcg
FI test.out
FZ = 211
FP /^\!\!NA_SEQUENCE 1\.0\n/
FP /^EMBL  Length: 100  Type: N  Check: 6856 \.\.\n/
FP /^   1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac\n/
//

ID seq-outusa-genbank
AP seqret
CL -auto ../../data/dna.embl genbank::test.out
FI test.out
FZ = 503
FP /^LOCUS       EMBL                     100 bp    DNA     linear   UNC \d\d-[A-Z][A-Z][A-Z]-20[0-9][0-9]\n/
FP /^DEFINITION  EMBL FORMAT DNA SEQUENCE\.\n/
FP /^ACCESSION   E10002\n/
FP /^VERSION     E10002\.34\n/
FP /^KEYWORDS    DNA binding protein; repressor\.\n/
FP /^SOURCE      Escherichia coli\n/
FP /^  ORGANISM  Escherichia coli\n/
FP /^            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/
FP /^            Escherichia\.\n/
FP /^ORIGIN\n/
FP /^        1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\n/
//

ID seq-out-genbank
AP seqret
CL -auto ../../data/dna.embl test.out -osf genbank
FI test.out
FZ = 503
FP /^LOCUS       EMBL                     100 bp    DNA     linear   UNC \d\d-[A-Z][A-Z][A-Z]-20[0-9][0-9]\n/
FP /^DEFINITION  EMBL FORMAT DNA SEQUENCE\.\n/
FP /^ACCESSION   E10002\n/
FP /^VERSION     E10002\.34\n/
FP /^KEYWORDS    DNA binding protein; repressor\.\n/
FP /^SOURCE      Escherichia coli\n/
FP /^  ORGANISM  Escherichia coli\n/
FP /^            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/
FP /^            Escherichia\.\n/
FP /^ORIGIN\n/
FP /^        1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\n/
//

ID seq-outusa-gff
AP seqret
CL -auto ../../data/dna.embl gff::test.out
FI test.out
FZ = 257
FP /^##gff-version 3\n/
FP /^##sequence-region EMBL 1 100\n/
FP /^#\!Source-version EMBOSS [0-9\.]+\n/
FP /^#\!Date [0-9\-]+\n/
FP /^#\!Type DNA\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-out-gff
AP seqret
CL -auto ../../data/dna.embl test.out -osf gff
FI test.out
FZ = 257
FP /^##gff-version 3\n/
FP /^##sequence-region EMBL 1 100\n/
FP /^#\!Source-version EMBOSS [0-9\.]+\n/
FP /^#\!Date [0-9\-]+\n/
FP /^#\!Type DNA\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-outusa-ig
AP seqret
CL -auto ../../data/dna.embl ig::test.out
FI test.out
FZ = 145
FP /;EMBL FORMAT DNA SEQUENCE, 100 bases\n/
FP /EMBL\n/
FP /gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt1\n/
//

ID seq-out-ig
AP seqret
CL -auto ../../data/dna.embl test.out -osf ig
FI test.out
FZ = 145
FP /;EMBL FORMAT DNA SEQUENCE, 100 bases\n/
FP /EMBL\n/
FP /gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt1\n/
//

ID seq-outusa-ncbi
AP seqret
CL -auto ../../data/dna.embl ncbi::test.out
FI test.out
FZ = 153
FP /^>gnl\|unk\|EMBL \(E10002\.34\) EMBL FORMAT DNA SEQUENCE\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-out-ncbi
AP seqret
CL -auto ../../data/dna.embl test.out -osf ncbi
FI test.out
FZ = 153
FP /^>gnl\|unk\|EMBL \(E10002\.34\) EMBL FORMAT DNA SEQUENCE\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-outusa-staden
AP seqret
CL -auto ../../data/dna.embl staden::test.out
FI test.out
FZ = 113
FP /<EMBL---->/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-out-staden
AP seqret
CL -auto ../../data/dna.embl test.out -osf staden
FI test.out
FZ = 113
FP /<EMBL---->/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-outusa-strider
AP seqret
CL -auto ../../data/dna.embl strider::test.out
FI test.out
FZ = 166
FP /^; ### from DNA Strider ;-\)\n/
FP /^; DNA sequence  EMBL, 100 bases\n/
FP /^;\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtac\n/
//

ID seq-out-strider
AP seqret
CL -auto ../../data/dna.embl test.out -osf strider
FI test.out
FZ = 166
FP /^; ### from DNA Strider ;-\)\n/
FP /^; DNA sequence  EMBL, 100 bases\n/
FP /^;\n/
FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtac\n/
//

ID seq-outusa-swiss
AP seqret
CL -auto ../../data/prot.swiss swiss::test.out
FI test.out
FZ = 288
FP /^ID   FASTA                   Unreviewed;         100 AA\.\n/
FP /^AC   S00001;\n/
FP /^DE   FASTA FORMAT PROTEIN SEQUENCE\n/
FP /^SQ   SEQUENCE   100 AA;  11907 MW;  DCEF6AA9E9BA19B4 CRC64;\n/
FP /^     ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/
FP /^     ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/
//

ID seq-out-swiss
AP seqret
CL -auto ../../data/prot.swiss test.out -osf swiss
FI test.out
FZ = 288
FP /^ID   FASTA                   Unreviewed;         100 AA\.\n/
FP /^AC   S00001;\n/
FP /^DE   FASTA FORMAT PROTEIN SEQUENCE\n/
FP /^SQ   SEQUENCE   100 AA;  11907 MW;  DCEF6AA9E9BA19B4 CRC64;\n/
FP /^     ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/
FP /^     ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/
//

ID seq-outusa-text
AP seqret
CL -auto ../../data/dna.embl text::test.out
FI test.out
FZ = 102
FP /^gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-out-text
AP seqret
CL -auto ../../data/dna.embl test.out -osf text
FI test.out
FZ = 102
FP /^gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/
//

ID seq-outmultiusa-acedb
AP seqret
CL -auto ../../data/dna.m-embl acedb::test.out
FI test.out
FZ = 420
FP 3 /^DNA : "FASTAM[1-3]"/
//

ID seq-outmulti-acedb
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf acedb
FI test.out
FZ = 420
FP 3 /^DNA : "FASTAM[1-3]"/
//

ID seq-outmultiusa-asn1
AP seqret
CL -auto ../../data/dna.m-embl asn1::test.out
FI test.out
FZ = 957
FP 3 /^    id \{ local id 1 \},/
FP 3 /^    descr { title "FASTA FORMAT DNA SEQUENCE F3000[1-3]" },\n/
FP /^    descr { title "FASTA FORMAT DNA SEQUENCE F30003" },\n/
//

ID seq-outmulti-asn1
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf asn1
FI test.out
FZ = 957
FP 3 /^    id \{ local id 1 \},/
FP 3 /^    descr { title "FASTA FORMAT DNA SEQUENCE F3000[1-3]" },\n/
FP /^    descr { title "FASTA FORMAT DNA SEQUENCE F30003" },\n/
//

ID seq-outmultiusa-clustal
AP seqret
CL -auto ../../data/dna.m-embl clustal::test.out
FI test.out
FZ = 664
FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/
FP /^FASTAM2         ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-outmulti-clustal
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf clustal
FI test.out
FZ = 664
FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/
FP /^FASTAM2         ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/
//

ID seq-outmultiusa-clustalprot
AP seqret
CL -auto ../../data/prot.m-swiss clustal::test.out
FI test.out
FZ = 584
FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/
FP /^SWISSM2         AACCDDEEFFGGHHIIKKLLMMNNPPQQRRSSTTVVWWYYAACCDDEEFFGGHHIIKKLL\n/
FP 3 /^\n/
FP 1 /^                                                                            \n/
//

ID seq-outmulti-clustalprot
AP seqret
CL -auto ../../data/prot.m-swiss test.out -osf clustal
FI test.out
FZ = 584
FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/
FP /^SWISSM2         AACCDDEEFFGGHHIIKKLLMMNNPPQQRRSSTTVVWWYYAACCDDEEFFGGHHIIKKLL\n/
FP 3 /^\n/
FP 1 /^                                                                            \n/
//

ID seq-outmultiusa-codata
AP seqret
CL -auto ../../data/dna.m-embl codata::test.out
FI test.out
FZ = 1410
FP 3 /^ENTRY           FASTAM[1-3] \n/
FP 3 /^\/\/\/\n/
//

ID seq-outmulti-codata
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf codata
FI test.out
FZ = 1410
FP 3 /^ENTRY           FASTAM[1-3] \n/
FP 3 /^\/\/\/\n/
//

ID seq-outmultiusa-debug
AP seqret
CL -auto ../../data/dna.m-embl debug::test.out
FI test.out
FZ = 3051
FP 3 /^  Name: 'FASTAM[1-3]'\n/
FP 3 /^  Accession: 'F3000[1-3]'\n/
FP /^  Entryname: 'FASTAM3'\n/
FP 3 /^  Usa: 'debug::test\.out'\n/
FP 3 /^  Input format: 'embl'\n/
FP 3 /^  Ufo: ''\n/
FP 3 /^  Entryname: 'FASTAM[1-3]'\n/
FP 3 /^  File name: 'test\.out'\n/
FP 3 /^  Extension: 'fasta'\n/
//

ID seq-outmulti-debug
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf debug
FI test.out
FZ = 3030
FP 3 /^  Name: 'FASTAM[1-3]'\n/
FP 3 /^  Accession: 'F3000[1-3]'\n/
FP /^  Entryname: 'FASTAM3'\n/
FP 3 /^  Usa: 'test\.out'\n/
FP 3 /^  Input format: 'embl'\n/
FP 3 /^  Ufo: ''\n/
FP 3 /^  Entryname: 'FASTAM[1-3]'\n/
FP 3 /^  File name: 'test\.out'\n/
FP 3 /^  Extension: 'debug'\n/
//

ID seq-outmultiusa-embl
AP seqret
CL -auto ../../data/dna.m-embl embl::test.out
FI test.out
FZ = 1023
FP 3 /^ID   F3000[1-3]; SV 1; linear; unassigned DNA; STD; UNC; 120 BP\.\n/
FP 3 /^AC   F3000[1-3];\n/
FP /^AC   F30003;\n/
FP /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;\n/
//

ID seq-outmulti-embl
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf embl
FI test.out
FZ = 1023
FP 3 /^ID   F3000[1-3]; SV 1; linear; unassigned DNA; STD; UNC; 120 BP\.\n/
FP 3 /^AC   F3000[1-3];\n/
FP /^AC   F30003;\n/
FP /^SQ   Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;\n/
//

ID seq-outmultiusa-fasta
AP seqret
CL -auto ../../data/dna.m-embl fasta::test.out
FI test.out
FZ = 513
FP 3 /^>FASTAM[1-3] F3000[1-3] FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/
FP /^>FASTAM3 F30003 FASTA FORMAT DNA SEQUENCE F30003\n/
//

ID seq-outmulti-fasta
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf fasta
FI test.out
FZ = 513
FP 3 /^>FASTAM[1-3] F3000[1-3] FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/
FP /^>FASTAM3 F30003 FASTA FORMAT DNA SEQUENCE F30003\n/
//

ID seq-outmultiusa-fitch
AP seqret
CL -auto ../../data/dna.m-embl fitch::test.out
FI test.out
FZ = 543
FP 3 /^FASTAM[1-3], 120 bases\n/
FP /^FASTAM1, 120 bases\n/
FP /^ ACG TAC GTA CGT ACG TAC GT- --- ACG TAC GTA CGT ACG TAC GTA CGT ACG TAC GTA CGT\n/
//

ID seq-outmulti-fitch
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf fitch
FI test.out
FZ = 543
FP 3 /^FASTAM[1-3], 120 bases\n/
FP /^FASTAM1, 120 bases\n/
FP /^ ACG TAC GTA CGT ACG TAC GT- --- ACG TAC GTA CGT ACG TAC GTA CGT ACG TAC GTA CGT\n/
//

ID seq-outmultiusa-gcg
AP seqret
CL -auto ../../data/dna.m-embl gcg::test.out
FI test.out
FZ = 750
FP 3 /^!!NA_SEQUENCE 1\.0\n/
FP /^FASTAM1  Length: 120  Type: N  Check: 8587 \.\.\n/
FP /^FASTAM2  Length: 120  Type: N  Check: 6178 \.\.\n/
FP /^FASTAM3  Length: 120  Type: N  Check: 8431 \.\.\n/
FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/
//

ID seq-outmulti-gcg
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf gcg
FI test.out
FZ = 750
FP 3 /^!!NA_SEQUENCE 1\.0\n/
FP /^FASTAM1  Length: 120  Type: N  Check: 8587 \.\.\n/
FP /^FASTAM2  Length: 120  Type: N  Check: 6178 \.\.\n/
FP /^FASTAM3  Length: 120  Type: N  Check: 8431 \.\.\n/
FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/
//

ID seq-outmultiusa-genbank
AP seqret
CL -auto ../../data/dna.m-embl genbank::test.out
FI test.out
FZ = 921
FP 3 /^LOCUS       FASTAM[1-3] /
FP /^LOCUS       FASTAM3 /
FP 3 /^ACCESSION   F3000[1-3]\n/
FP /^ACCESSION   F30003\n/
FP 3 /^\/\/\n/
//

ID seq-outmulti-genbank
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf genbank
FI test.out
FZ = 921
FP 3 /^LOCUS       FASTAM[1-3] /
FP /^LOCUS       FASTAM3 /
FP 3 /^ACCESSION   F3000[1-3]\n/
FP /^ACCESSION   F30003\n/
FP 3 /^\/\/\n/
//

ID seq-outmultiusa-gff
AP seqret
CL -auto ../../data/dna.m-embl gff::test.out
FI test.out
FZ = 864
FP 3 /^##sequence-region FASTAM[1-3] 1 120\n/
FP 3 /^#\!Type DNA\n/
FP /^##sequence-region FASTAM2 1 120\n/
FP 3 /^##FASTA\n/
//

ID seq-outmulti-gff
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf gff
FI test.out
FZ = 864
FP 3 /^##sequence-region FASTAM[1-3] 1 120\n/
FP 3 /^#\!Type DNA\n/
FP /^##sequence-region FASTAM2 1 120\n/
FP 3 /^##FASTA\n/
//

ID seq-outmultiusa-gffprot
AP seqret
CL -auto ../../data/prot.m-swiss gff::test.out
FI test.out
FZ = 765
FP 3 /^#!Type Protein\n/
FP 3 /^##sequence-region SWISSM[1-3] 1 \d+\n/
FP 1 /^##sequence-region SWISSM2 1 80\n/
FP 3 /^#!Type Protein\n/
//

ID seq-outmulti-gffprot
AP seqret
CL -auto ../../data/prot.m-swiss test.out -osf gff
FI test.out
FZ = 765
FP 3 /^#!Type Protein\n/
FP 3 /^##sequence-region SWISSM[1-3] 1 \d+\n/
FP 1 /^##sequence-region SWISSM2 1 80\n/
FP 3 /^#!Type Protein\n/
//

ID seq-outmultiusa-hennig86
AP seqret
CL -auto ../../data/dna.m-embl hennig86::test.out
FI test.out
FZ = 432
FP /^xread\n/
FP /^' Written by EMBOSS [0-9][0-9]\/[01][0-9]\/[0-9][0-9] '\n/
FP /^120 3\n/
FP 3 /^FASTAM[1-3]\n/
FP /^FASTAM2\n/
FP /^03210321032103210321\?\?\?\?032103210321032103210321032103210321032103210321032103210321032103210321032103210321123003210321\n/
FP /^;\n/
//

ID seq-outmulti-hennig86
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf hennig86
FI test.out
FZ = 432
FP /^xread\n/
FP /^' Written by EMBOSS [0-9][0-9]\/[01][0-9]\/[0-9][0-9] '\n/
FP /^120 3\n/
FP 3 /^FASTAM[1-3]\n/
FP /^FASTAM2\n/
FP /^03210321032103210321\?\?\?\?032103210321032103210321032103210321032103210321032103210321032103210321032103210321123003210321\n/
FP /^;\n/
//

ID seq-outmultiusa-jackknifer
AP seqret
CL -auto ../../data/dna.m-embl jackknifer::test.out
FI test.out
FZ = 590
FP /^' Written by EMBOSS [0-9\/]+ \n/
FP 3 /^\(FASTAM3\)            [ACGT.\-]+\n/
//

ID seq-outmulti-jackknifer
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf jackknifer
FI test.out
FZ = 590
FP /^' Written by EMBOSS [0-9\/]+ \n/
FP 3 /^\(FASTAM3\)            [ACGT.\-]+\n/
//

ID seq-outmultiusa-mega
AP seqret
CL -auto ../../data/dna.m-embl mega::test.out
FI test.out
FZ = 722
FP /^#mega\n/
FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/
FP 9 /^#FASTAM[1-3] [ACGT.\-]+\n/
FP 7 /^\n/
//

ID seq-outmulti-mega
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf mega
FI test.out
FZ = 722
FP /^#mega\n/
FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/
FP 9 /^#FASTAM[1-3] [ACGT.\-]+\n/
FP 7 /^\n/
//

ID seq-outmultiusa-meganon
AP seqret
CL -auto ../../data/dna.m-embl meganon::test.out
FI test.out
FZ = 633
FP /^#mega\n/
FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/
FP /^#FASTAM2\n/
FP 3 /^#FASTAM[1-3]\n/
//

ID seq-outmulti-meganon
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf meganon
FI test.out
FZ = 633
FP /^#mega\n/
FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/
FP /^#FASTAM2\n/
FP 3 /^#FASTAM[1-3]\n/
//

ID seq-outmultiusa-msf
AP seqret
CL -auto ../../data/dna.m-embl msf::test.out
FI test.out
FZ = 880
FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/
FP /^  test\.out MSF: 120 Type: N [0-9\/]+ CompCheck: 3196 \.\.\n/
FP /^  Name: FASTAM1    Len: 120  Check: 8587 Weight: 1\.00\n/
FP /^  Name: FASTAM2    Len: 120  Check: 6178 Weight: 1\.00\n/
FP /^  Name: FASTAM3    Len: 120  Check: 8431 Weight: 1\.00\n/
FP /^\/\/\n/
FP /^           1                                               50\n/
FP 3 /^FASTAM3    [ACGT\-]+\n/
//

ID seq-outmulti-msf
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf msf
FI test.out
FZ = 880
FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/
FP /^  test\.out MSF: 120 Type: N [0-9\/]+ CompCheck: 3196 \.\.\n/
FP /^  Name: FASTAM1    Len: 120  Check: 8587 Weight: 1\.00\n/
FP /^  Name: FASTAM2    Len: 120  Check: 6178 Weight: 1\.00\n/
FP /^  Name: FASTAM3    Len: 120  Check: 8431 Weight: 1\.00\n/
FP /^\/\/\n/
FP /^           1                                               50\n/
FP 3 /^FASTAM3    [ACGT\-]+\n/
//

ID seq-outmulti-msf-noalign
AP seqret
CL -auto "tembl:M1190*" test.out -osf msf
FI test.out
FZ = 3884
FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/
FP /^  test\.out MSF: 724 Type: N [0-9/]+ CompCheck: 3521 \.\.\n/
FP 3 /^  Name: M1190/
FP /^           1                                               50\n/
FP 11 /^M11904 +[ACGTacgt\-]+\n/
FP 1 /^M11904 +[ACGTacgt\-]+[~]+\n/
FP 3 /^M11904 +[~]+\n/
//

ID seq-outmultiusa-msfprot
AP seqret
CL -auto ../../data/prot.m-swiss msf::test.out
FI test.out
FZ = 752
FP /^!!AA_MULTIPLE_ALIGNMENT 1\.0\n/
FP /^  test\.out MSF:  100 Type: P [0-9\/]+ CompCheck: 4147 \.\.\n/
FP /^  Name: SWISSM1    Len: 100  Check: 1414 Weight: 1\.00\n/
FP /^  Name: SWISSM2    Len: 100  Check: 1993 Weight: 1\.00\n/
FP /^  Name: SWISSM3    Len: 100  Check:  740 Weight: 1\.00\n/
FP /^\/\/\n/
FP /^           1                                               50\n/
FP 2 /^SWISSM2    [A-Z~]+\n/
//

ID seq-outmulti-msfprot
AP seqret
CL -auto ../../data/prot.m-swiss test.out -osf msf
FI test.out
FZ = 752
FP /^!!AA_MULTIPLE_ALIGNMENT 1\.0\n/
FP /^  test\.out MSF:  100 Type: P [0-9\/]+ CompCheck: 4147 \.\.\n/
FP /^  Name: SWISSM1    Len: 100  Check: 1414 Weight: 1\.00\n/
FP /^  Name: SWISSM2    Len: 100  Check: 1993 Weight: 1\.00\n/
FP /^  Name: SWISSM3    Len: 100  Check:  740 Weight: 1\.00\n/
FP /^\/\/\n/
FP /^           1                                               50\n/
FP 2 /^SWISSM2    [A-Z~]+\n/
//

ID seq-outmultiusa-nexus
AP seqret
CL -auto ../../data/dna.m-embl nexus::test.out
FI test.out
FZ = 756
FP /^#NEXUS\n/
FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/
FP /^begin data;\n/
FP /^dimensions ntax=3 nchar=120;\n/
FP /^format interleave datatype=DNA missing=N gap=-;\n/
FP /^matrix\n/
FP /^;\n/
FP /^end;\n/
FP /^begin assumptions;\n/
FP /^options deftype=unord;\n/
FP 3 /^FASTAM2              [ACGT\-]+\n/
//

ID seq-outmulti-nexus
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf nexus
FI test.out
FZ = 756
FP /^#NEXUS\n/
FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/
FP /^begin data;\n/
FP /^dimensions ntax=3 nchar=120;\n/
FP /^format interleave datatype=DNA missing=N gap=-;\n/
FP /^matrix\n/
FP /^;\n/
FP /^end;\n/
FP /^begin assumptions;\n/
FP /^options deftype=unord;\n/
FP 3 /^FASTAM2              [ACGT\-]+\n/
//

ID seq-outmultiusa-nexusnon
AP seqret
CL -auto ../../data/dna.m-embl nexusnon::test.out
FI test.out
FZ = 572
FP /^#NEXUS\n/
FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/
FP /^begin data;\n/
FP /^dimensions ntax=3 nchar=120;\n/
FP /^format datatype=DNA missing=N gap=-;\n/
FP /^matrix\n/
FP 3 /^FASTAM[1-3]\n/
FP 3 /^[ACGT\-]+\n/
FP /^;\n/
FP /^end;\n/
FP /^begin assumptions;\n/
FP /^options deftype=unord;\n/
//

ID seq-outmulti-nexusnon
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf nexusnon
FI test.out
FZ = 572
FP /^#NEXUS\n/
FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/
FP /^begin data;\n/
FP /^dimensions ntax=3 nchar=120;\n/
FP /^format datatype=DNA missing=N gap=-;\n/
FP /^matrix\n/
FP 3 /^FASTAM[1-3]\n/
FP 3 /^[ACGT\-]+\n/
FP /^;\n/
FP /^end;\n/
FP /^begin assumptions;\n/
FP /^options deftype=unord;\n/
//

ID seq-outmultiusa-phylip
AP seqret
CL -auto ../../data/dna.m-embl phylip::test.out
FI test.out
FZ = 495
FP /^ 3 120\n/
FP /^FASTAM1   ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/
FP 6 /^          [ACGT \-]+\n/
//

ID seq-outmulti-phylip
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf phylip
FI test.out
FZ = 495
FP /^ 3 120\n/
FP /^FASTAM1   ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/
FP 6 /^          [ACGT \-]+\n/
//

ID seq-outmultiusa-phylipnon
AP seqret
CL -auto ../../data/dna.m-embl phylipnon::test.out
FI test.out
FZ = 492
FP /^3 120\n/
FP /^FASTAM1   ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/
FP 6 /^          [ACGT \-]+\n/
FP / GTACGTACGT\nFASTAM2/
//

ID seq-outmulti-phylipnon
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf phylipnon
FI test.out
FZ = 492
FP /^3 120\n/
FP /^FASTAM1   ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/
FP 6 /^          [ACGT \-]+\n/
FP / GTACGTACGT\nFASTAM2/
//

ID seq-outmultiusa-swiss
AP seqret
CL -auto ../../data/prot.m-swiss swiss::test.out
FI test.out
FZ =  810
FP 3 /^ID   SWISSM[1-3] +Unreviewed; +[0-9]+ AA\.\n/
FP /^ID   SWISSM2                 Unreviewed;          80 AA\.\n/
FP /^SQ   SEQUENCE   60 AA;  7151 MW;  FF73258FFC19CF5B CRC64;/
FP 3 /^\/\/\n/
//

ID seq-outmulti-swiss
AP seqret
CL -auto ../../data/prot.m-swiss test.out -osf swiss
FI test.out
FZ =  810
FP 3 /^ID   SWISSM[1-3] +Unreviewed; +[0-9]+ AA\.\n/
FP /^ID   SWISSM2                 Unreviewed;          80 AA\.\n/
FP /^SQ   SEQUENCE   60 AA;  7151 MW;  FF73258FFC19CF5B CRC64;/
FP 3 /^\/\/\n/
//

ID seq-outmultiusa-ncbi
AP seqret
CL -auto ../../data/dna.m-embl ncbi::test.out
FI test.out
FZ = 543
FP 3 /^>gnl\|unk\|FASTAM[1-3] \(F3000[1-3]\) FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/
FP /^>gnl\|unk\|FASTAM2 \(F30002\) FASTA FORMAT DNA SEQUENCE F30002\n/
//

ID seq-outmulti-ncbi
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf ncbi
FI test.out
FZ = 543
FP 3 /^>gnl\|unk\|FASTAM[1-3] \(F3000[1-3]\) FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/
FP /^>gnl\|unk\|FASTAM2 \(F30002\) FASTA FORMAT DNA SEQUENCE F30002\n/
//

ID seq-outmultiusa-nbrf
AP seqret
CL -auto ../../data/dna.m-embl nbrf::test.out
FI test.out
FZ = 579
FP 3 /^>D1;FASTAM[1-3]\n/
FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/
FP /^FASTA FORMAT DNA SEQUENCE F30001, 120 bases\n/
FP /^ ACGTACGTTG CAACGTACGT\*\n/
//

ID seq-outmulti-nbrf
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf nbrf
FI test.out
FZ = 579
FP 3 /^>D1;FASTAM[1-3]\n/
FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/
FP /^FASTA FORMAT DNA SEQUENCE F30001, 120 bases\n/
FP /^ ACGTACGTTG CAACGTACGT\*\n/
//

ID seq-outmultiusa-ig
AP seqret
CL -auto ../../data/dna.m-embl ig::test.out
FI test.out
FZ = 531
FP /^;FASTA FORMAT DNA SEQUENCE F30002, 120 bases\n/
FP 3 /^;FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/
FP /^FASTAM2\n/
FP 3 /^FASTAM[1-3]\n/
FP /^ACGTACGTACGTACGTACGT1\n/
//

ID seq-outmulti-ig
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf ig
FI test.out
FZ = 531
FP /^;FASTA FORMAT DNA SEQUENCE F30002, 120 bases\n/
FP 3 /^;FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/
FP /^FASTAM2\n/
FP 3 /^FASTAM[1-3]\n/
FP /^ACGTACGTACGTACGTACGT1\n/
//

ID seq-outmultiusa-strider
AP seqret
CL -auto ../../data/dna.m-embl strider::test.out
FI test.out
FZ = 570
FP /^; ### from DNA Strider ;-\)\n/
FP 3 /^; DNA sequence  FASTAM[1-3], 120 bases\n/
FP /^; DNA sequence  FASTAM2, 120 bases\n/
FP /^;\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-outmulti-strider
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf strider
FI test.out
FZ = 570
FP /^; ### from DNA Strider ;-\)\n/
FP 3 /^; DNA sequence  FASTAM[1-3], 120 bases\n/
FP /^; DNA sequence  FASTAM2, 120 bases\n/
FP /^;\n/
FP /^ACGTACGTACGTACGTACGT\n/
//

ID seq-outmultiusa-treecon
AP seqret
CL -auto ../../data/dna.m-embl treecon::test.out
FI test.out
FZ = 391
FP /^120\n/
FP 3 /^FASTAM[1-3]\n/
FP /^FASTAM2\n/
FP /^ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCAACGTACGT\n/
//

ID seq-outmulti-treecon
AP seqret
CL -auto ../../data/dna.m-embl test.out -osf treecon
FI test.out
FZ = 391
FP /^120\n/
FP 3 /^FASTAM[1-3]\n/
FP /^FASTAM2\n/
FP /^ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCAACGTACGT\n/
//

ID seq-offset
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat%1864
FI test.out
FZ = 11907
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 5 /^ID/
FI stderr
FZ = 0
//

ID seq-offset-zero
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat%0
FI test.out
FZ = 13390
FP /^ID   L48662; /
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 6 /^ID/
FI stderr
FZ = 0
//

ID seq-ftp
AP seqret
CL -auto -out test.out -osf embl ftp://emboss.open-bio.org/pub/EMBOSS/testdata/rod.dat
FI test.out
FZ = 13390
FP /^ID   L48662; /
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 6 /^ID/
FI stderr
FZ = 0
//

ID seq-ftp-bad
ER 1
AP seqret
CL -auto -out test.out -osf embl ftp://emboss.open-bio.org/pub/EMBOSS/testdata/rod.none
FI stderr
FC = 3
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /^Error: Cannot open FTP connection 'ftp://emboss.open-bio.org/pub/EMBOSS/testdata/rod.none'\n/
FP /^Error: Unable to read sequence 'ftp://emboss.open-bio.org/pub/EMBOSS/testdata/rod.none'\n/
//

ID seq-ftp-ioffset
AP seqret
CL -auto -out test.out -osf embl ftp://emboss.open-bio.org/pub/EMBOSS/testdata/rod.dat -ioffset 1864
FI test.out
FZ = 11907
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 5 /^ID/
FI stderr
FZ = 0
//

ID seq-http
AP seqret
CL -auto -out test.out -osf embl http://emboss.open-bio.org/downloads/rod.dat
FI test.out
FZ = 13390
FP /^ID   L48662; /
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 6 /^ID/
FI stderr
FZ = 0
//

ID seq-http-bad
ER 1
AP seqret
CL -auto -out test.out -osf embl http://emboss.open-bio.org/downloads/rod.none
FI stderr
FC = 3
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /^Error: Cannot open HTTP connection 'http://emboss.open-bio.org/downloads/rod.none'\n/
FP /^Error: Unable to read sequence 'http://emboss.open-bio.org/downloads/rod.none'\n/
//

ID seq-http-ioffset
AP seqret
CL -auto -out test.out -osf embl http://emboss.open-bio.org/downloads/rod.dat -ioffset 1864
FI test.out
FZ = 11907
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 5 /^ID/
FI stderr
FZ = 0
//

#####################################################
# Test the query part of USAs
#####################################################

ID seqret-query-direct-fail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:bad:L48662
FI stderr
FZ = 238
FP /Error: Query '\.\.\/\.\.\/embl\/rod\.dat:bad:L48662' query field 'bad' not defined for datatype 'sequence'/
FP /Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:bad:L48662'/
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-name
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:L48662
FI test.out
FZ = 1483
FP /^ID   L48662;/
FP 1 /^ID/
//

ID seqret-query-direct-name2
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:Z46957
FI test.out
FZ = 3312
FP /^ID   Z46957; /
FP 1 /^ID/
//

ID seqret-query-direct-namefail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:FAIL
FI stderr
FZ = 133
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:FAIL'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-id
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:id:L48662
FI test.out
FZ = 1483
FP /^ID   L48662; /
FP 1 /^ID/
//

ID seqret-query-direct-id2
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ID:Z46957
FI test.out
FZ = 3312
FP /^ID   Z46957; /
FP 1 /^ID/
//

ID seqret-query-direct-idfail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ID:FAIL
FI stderr
FZ = 136
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ID:FAIL'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-acc
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:L48662
FI test.out
FZ = 1483
FP /^ID   L48662; /
FP 1 /^ID/
//

ID seqret-query-direct-acc2
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:Z46957
FI test.out
FZ = 3312
FP /^ID   Z46957; /
FP 1 /^ID/
//

ID seqret-query-direct-accfail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:Z99999
FI stderr
FZ = 139
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ACC:Z99999'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-accfail2
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:99999Z
FI stderr
FZ = 139
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ACC:99999Z'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-sv
AP seqret
CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:SV:L48662*"
FI test.out
FZ = 1483
FP /^ID   L48662; /
FP 1 /^ID/
//

ID seqret-query-direct-sv2
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:Z46957.1
FI test.out
FZ = 3312
FP /^ID   Z46957; /
FP 1 /^ID/
//

ID seqret-query-direct-svfail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:Z99999.1
FI stderr
FZ = 140
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:SV:Z99999\.1'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-des
AP seqret
CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:DES:*receptor*"
FI test.out
FZ = 2956
FP /^ID   U68037; /
FP 1 /^ID/
//

ID seqret-query-direct-des2
AP seqret
CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:DES:*norvegicus*"
FI test.out
FZ = 11907
FP /^ID   Z46957; /
FP 5 /^ID/
//

ID seqret-query-direct-desfail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:lynam
FI stderr
FZ = 138
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:DES:lynam'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-deswordstart
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:Mus
FI test.out
FZ = 1483
FP /^ID   L48662; /
FP 1 /^ID/
//

ID seqret-query-direct-deswordmid
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:mrna
FI test.out
FZ = 7751
FP /^ID   L48662; /
FP 3 /^ID/
//

ID seqret-query-direct-deswordend
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:receptor
FI test.out
FZ = 2956
FP /^ID   U68037; /
FP 1 /^ID/
//

ID seqret-query-direct-key
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:KEY:rhodopsin
FI test.out
FZ = 3312
FP /^ID   Z46957; /
FP 1 /^ID/
//

ID seqret-query-direct-keyfail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:KEY:CHAIN
FI stderr
FZ = 138
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:KEY:CHAIN'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-direct-org
AP seqret
CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:ORG:Mus*"
FI test.out
FZ = 1483
FP /^ID   L48662; /
FP 1 /^ID/
//

ID seqret-query-direct-org2
AP seqret
CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:ORG:Rattus*"
FI test.out
FZ = 11907
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 5 /^ID/
//

ID seqret-query-direct-org3
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:Rodentia
FI test.out
FZ = 13390
FP /^ID   L48662; /
FP /^ID   Z46957; /
FP /^ID   U68037; /
FP 6 /^ID/
//

ID seqret-query-direct-orgfail
ER 1
AP seqret
CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:HOMO
FI stderr
FZ = 137
FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ORG:HOMO'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-srs-id
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrs-ID:AB000095
FI test.out
FZ = 3701
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srs-acc
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrs-ACC:AB000095
FI test.out
FZ = 3701
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srs-sv
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrs-SV:AB000095.1
FI test.out
FZ = 3701
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srs-name
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrs:AB000095
FI test.out
FZ = 3701
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srs-fail
CC Requires a local SRS installation
RQ srs
ER 1
AP seqret
CL -auto -out test.out -osf embl qasrs-id:OLD
FI stderr
FZ = 116
FP /^Error: Unable to read sequence 'qasrs-id:OLD'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-srsfasta-id
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrsfasta-ID:AB000095
FI test.out
FZ = 3407
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srsfasta-acc
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrsfasta-ACC:AB000095
FI test.out
FZ = 3407
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srsfasta-sv
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrsfasta-SV:AB000095.1
FI test.out
FZ = 3407
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srsfasta-name
CC Requires a local SRS installation
RQ srs
AP seqret
CL -auto -out test.out -osf embl qasrsfasta:AB000095
FI test.out
FZ = 3407
FP /^ID   AB000095 /
FP 1 /^ID /
//

ID seqret-query-srsfasta-fail
CC Requires a local SRS installation
RQ srs
ER 1
AP seqret
CL -auto -out test.out -osf embl qasrsfasta-id:OLD
FI stderr
FZ = 121
FP /^Error: Unable to read sequence 'qasrsfasta-id:OLD'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-srswww-id
AP seqret
CC Requires http access to EBI SRS server
CL -auto -out test.out -osf sw qasrswww-ID:last_ecoli
FI test.out
FZ = 4534
FP /^ID   LAST_ECOLI +Reviewed; +228 AA\.\n/
FP 1 /^ID /
//

ID seqret-query-srswww-acc
AP seqret
CC Requires http access to EBI SRS server
CL -auto -out test.out -osf sw qasrswww-ACC:P37005
FI test.out
FZ = 4534
FP /^ID   LAST_ECOLI /
FP 1 /^ID /
//

ID seqret-query-srswww-sv
AP seqret
CC Requires http access to EBI SRS server
CL -auto -out test.out -osf sw qasrswww-SV:P37005.2
FI test.out
FZ = 4534
FP /^ID   LAST_ECOLI /
FP 1 /^ID /
//

ID seqret-query-srswww-name
AP seqret
CC Requires http access to EBI SRS server
CL -auto -out test.out -osf sw qasrswww:LAST_ECOLI
FI test.out
FZ = 4534
FP /^ID   LAST_ECOLI /
FP 1 /^ID /
//

ID seqret-query-srswww-fail
ER 1
AP seqret
CC Requires http access to EBI SRS server
CL -auto -out test.out -osf sw qasrswww-id:OLD
FI stderr
FZ = 119
FP /^Error: Unable to read sequence 'qasrswww-id:OLD'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-filename-simple
AP seqret
CL -auto -out test.out -osf embl "../../data/dna.embl"
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 16
FP 1 /^ID   /
FP /^ID   E10002; /
//

ID seqret-query-filename-wild
AP seqret
CL -auto -out test.out -osf embl "../../data/*.embl"
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 44
FP 2 /^ID   /
FP /^ID   E10002; /
//

ID seqret-query-filename-wildid
AP seqret
CL -auto -out test.out -osf embl "../../data/*.embl:e10002"
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 16
FP 1 /^ID   /
FP /^ID   E10002; /
//

ID seqret-query-filename-wildnoid
AP seqret
CL -auto -out test.out -osf embl "../../data/*.embl:abcde"
ER 1
FI stderr
FC = 2
FP /^Error: Unable to read sequence '\.\./\.\./data/\*\.embl:abcde'/
FP 0 /Warning: /
FP 1 /Error: /
FP 1 /Died: /
//

ID seqret-query-filename-wildnofile
AP seqret
CL -auto -out test.out -osf embl "../../data/*.nofiles"
ER 1
FI stderr
FC = 3
FP /^Error: Failed to open filename '\.\./\.\./data/\*\.nofiles'/
FP /^Error: Unable to read sequence '\.\./\.\./data/\*\.nofiles'/
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
//

ID seqret-query-filename-wildnofileid
AP seqret
CL -auto -out test.out -osf embl "../../data/*.nofiles:e10002"
ER 1
FI stderr
FC = 3
FP /^Error: Failed to open filename '\.\./\.\./data/\*\.nofiles'/
FP /^Error: Unable to read sequence '\.\./\.\./data/\*\.nofiles:e10002'/
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
//

ID seqret-query-filename-home
AP seqret
PP cp ../../data/dna.embl ~/seqret-query-filename-home.embl
QQ rm ~/seqret-query-filename-home.embl
CL -auto -out test.out -osf embl "~/seqret-query-filename-home.embl"
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 16
FP 1 /^ID   /
FP /^ID   E10002; /
//

####################################################
# End of query USA tests
####################################################


####################################################
# seqret examples for documentation
####################################################

ID seqret-ex
UC Extract an entry from a database and write it to a file: 
AP seqret
IN tembl:x65923
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.fasta
FP /X65923/
//

ID seqret-ex2
UC Display the contents of the sequence on the screen:
AP seqret
IN tembl:x65923
IN stdout
FI stdout
FP /X65923/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID seqret-ex3
UC Write the result in GCG format by using the qualifier '-osformat'.
AP seqret
CL -osf gcg
IN tembl:x65923
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.gcg
FP /X65923/
//

ID seqret-ex4
UC Write the result in GCG format by specifying the format
UC in the output USA on the command line.
AP seqret
CL -outseq gcg::x65923.gcg
IN tembl:x65923
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.gcg
FP /X65923/
//

ID seqret-ex5
UC Write the result in GCG format by specifying the format
UC in the output USA at the prompt.
AP seqret
IN tembl:x65923
IN gcg::x65923.gcg
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.gcg
FP /X65923/
//

ID seqret-ex6
UC Write the reverse-complement of a sequence:
AP seqret
CL -srev
IN tembl:x65923
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.fasta
FP /X65923/
//

ID seqret-ex7
UC Extract the bases between the positions starting at 5 and ending at 25:
AP seqret
CL -sbegin 5 -send 25
IN tembl:x65923
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.fasta
FP /X65923/
//

ID seqret-ex8
UC Extract the bases between the positions starting at 5
UC and ending at 5 bases before the end of the sequence:
AP seqret
CL -sbegin 5 -send -5
IN tembl:x65923
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.fasta
FP /X65923/
//

ID seqret-ex9
UC Read all entries in the database 'tembl' that start with 'h'
UC and write them to a file:
AP seqret
IN tembl:h*
IN hall.seq
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hall.seq
FP /H45989/
//

ID seqret-ex10
UC Read all entries in the database 'tembl' that start with 'ab'
UC and write them to a file.
UC In this example the specification is all done in the command line
UC and to stop Unix getting confused by the '*' character,
UC it has to have a backslash ('\') before it:
AP seqret
CL "tembl:ab*"  aball.seq
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI aball.seq
FP /^>AB000095/
FP 5 /^>/
//

ID seqret-ex11
UC seqret does not read in features by default because this results in
UC slightly faster performance.  If however you wish to read in features
UC with your sequence and write them out on output, using '-feature' will
UC change the default behaviour to use any features present in the sequence. 
UC N.B. use embl format for the output file as the default format 'fasta'
UC reports the features in gff (file "<seqname>.gff")
AP seqret
CL -feature
IN tembl:x65923
IN embl::x65923.embl
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.embl
FP /X65923/
//


ID seqret-circ1
AP seqret
CL -auto tembl:ab031077 embl::test.out
FI test.out
FP /^ID   .*circular/
//


ID seqret-circ2
AP seqret
CL -auto -scircular tembl:x65923 embl::test.out
FI test.out
FP /^ID   .*circular/
//


ID seqret-circ3
AP seqret
CL -auto -feature tembl:ab031077 gff3::test.out
FI test.out
FP /Is_circular[=]true;/
//


####################################################
# end of seqret examples for documentation
####################################################


ID seqretall-ex
AP seqret
CL -auto @../../data/eclac.list test.out -osf fasta
FI test.out
FZ = 15619
FP 1 /^>J01636/
FP 3 /^>V0029/
FP 5 /^>/
//

ID seqretall-ex2
AP seqret
CL -auto tembl:v00296 test.out -osf fasta
FI test.out
FP 1 /^>V00296/
//

#############################################################################

# should make output filename optional as it is rarely used

ID seqretsplit-ex
AP seqretsplit
CL tembl:m1190*
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI m11903.fasta
FZ = 861
FP /^>M11903 /
FI m11904.fasta
FZ = 710
FP /^>M11904 /
FI m11905.fasta
FZ = 654
FP /^>M11905 /
//

#####################################################
# Testing NCBI formatted ID lines are correctly split
#####################################################

ID seqret-ncbi-gb
AP seqret
CL ../../data/testids.ncbi:GENBANK test.out -auto
FI test.out
FP 1 /^>/
FP /^>GENBANK G12345 /
FP /^GENBANK$/
FZ = 58
//

ID seqret-ncbi-embl
AP seqret
CL ../../data/testids.ncbi:EMBL test.out -auto
FI test.out
FP 1 /^>/
FP /^>EMBL E12345 /
FP /^EMBL$/
FZ = 49
//

ID seqret-ncbi-ddbj
AP seqret
CL ../../data/testids.ncbi:DDBJ test.out -auto
FI test.out
FP 1 /^>/
FP /^>DDBJ D12345 /
FP /^DDB-$/
FZ = 49
//

ID seqret-ncbi-pir
AP seqret
CL ../../data/testids.ncbi:PIR test.out -auto
FI test.out
FP 1 /^>/
FP /^>PIR PIR/
FP /^PIR$/
FZ = 40
//

ID seqret-ncbi-prf
AP seqret
CL ../../data/testids.ncbi:PRF test.out -auto
FI test.out
FP 1 /^>/
FP /^>PRF Protein /
FP /^PRF$/
FZ = 58
//

ID seqret-ncbi-swissprt
AP seqret
CL ../../data/testids.ncbi:SWISS_PRT test.out -auto
FI test.out
FP 1 /^>/
FP /^>SWISS_PRT P01234/
FP /^SWISSPR-T$/
FZ = 64
//

ID seqret-ncbi-pdb
AP seqret
CL ../../data/testids.ncbi:2PDBA test.out -auto
FI test.out
FP 1 /^>/
FP /^>2PDBA PDB /
FP /^-PDB-A$/
FZ = 35
//

ID seqret-ncbi-pat
AP seqret
CL ../../data/testids.ncbi:12345 test.out -auto
FI test.out
FP 1 /^>/
FP /^>12345 Patent/
FP /^PAT-K$/
FZ = 39
//

ID seqret-ncbi-bbs
AP seqret
CL ../../data/testids.ncbi:GENINFO test.out -auto
FI test.out
FP 1 /^>/
FP /^>geninfo Geninfo/
FP /^GENINF-$/
FZ = 37
//

ID seqret-ncbi-gnl
AP seqret
CL ../../data/testids.ncbi:E1234 test.out -auto
FI test.out
FP 1 /^>/
FP /^>e1234 General/
FP /^GNLPID$/
FZ = 68
//

ID seqret-ncbi-ref1
AP seqret
CL ../../data/testids.ncbi:REF_12345 test.out -auto
FI test.out
FP 1 /^>/
FP /^>REF_12345 NP_007225\.1 /
FP /^REFSEQ$/
FZ = 54
//

ID seqret-ncbi-ref2
AP seqret
CL ../../data/testids.ncbi:NM_012488.1 test.out -auto
FI test.out
FP 1 /^>/
FP /^>NM_012488\.1 NM_012488\.1 /
FP /^REFSEQ$/
FZ = 70
//

ID seqret-ncbi-lcl
AP seqret
CL ../../data/testids.ncbi:LOCALID test.out -auto
FI test.out
FP 1 /^>/
FP /^>localid Local /
FP /^L-CALID$/
FZ = 53
//

ID seqret-ncbi-gi
AP seqret
CL ../../data/testids.ncbi:123456 test.out -auto
FI test.out
FP 1 /^>/
FP /^>123456 gi prefix/
FP /^GIPREFIX$/
FZ = 27
//

ID seqret-ncbi-gigb
AP seqret
CL ../../data/testids.ncbi:GIGENBANK test.out -auto
FI test.out
FP 1 /^>/
FP /^>GIGENBANK G67890 /
FP /^GIGENBANK$/
FZ = 52
//

ID seqret-ncbi-gisp
AP seqret
CL ../../data/testids.ncbi:GISWISS_PRT test.out -auto
FI test.out
FP 1 /^>/
FP /^>GISWISS_PRT P01234 /
FP /^GISWISSPR-T$/
FZ = 58
//

ID seqret-ncbi-gnlblast
AP seqret
CL ../../data/testids.ncbi:BLAST test.out -auto
FI test.out
FP 1 /^>/
FP /^>Blast formatdb /
FP /^BLAST$/
FZ = 46
//

#####################################################
# Testing NCBI formatted ID lines are correctly reproduced
#####################################################

ID seqret-ncbiout-gb
AP seqret
CL ../../data/testids.ncbi:GENBANK test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gb\|G12345\|GENBANK genbank /
FP /^GENBANK$/
FZ = 61
//

ID seqret-ncbiout-embl
AP seqret
CL ../../data/testids.ncbi:EMBL test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>emb\|E12345\|EMBL embl /
FP /^EMBL$/
FZ = 53
//

ID seqret-ncbiout-ddbj
AP seqret
CL ../../data/testids.ncbi:DDBJ test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>dbj\|D12345\|DDBJ DDBJ /
FP /^DDB-$/
FZ = 53
//

ID seqret-ncbiout-pir
AP seqret
CL ../../data/testids.ncbi:PIR test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>pir\|\|PIR /
FP /^PIR$/
FZ = 45
//

ID seqret-ncbiout-prf
AP seqret
CL ../../data/testids.ncbi:PRF test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>prf\|\|PRF /
FP /^PRF$/
FZ = 63
//

ID seqret-ncbiout-swissprt
AP seqret
CL ../../data/testids.ncbi:SWISS_PRT test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>sp\|P01234\|SWISS_PRT swissprot /
FP /^SWISSPR-T$/
FZ = 67
//

ID seqret-ncbiout-pdb
AP seqret
CL ../../data/testids.ncbi:2PDBA test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gnl\|pdb\|2PDBA PDB /
FP /^-PDB-A$/
FZ = 43
//

ID seqret-ncbiout-pat
AP seqret
CL ../../data/testids.ncbi:12345 test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gnl\|unk\|12345 Patent /
FP /^PAT-K$/
FZ = 47
//

ID seqret-ncbiout-bbs
AP seqret
CL ../../data/testids.ncbi:GENINFO test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gnl|unk|geninfo Geninfo /
FP /^GENINF-$/
FZ = 45
//

ID seqret-ncbiout-gnl
AP seqret
CL ../../data/testids.ncbi:E1234 test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gnl\|PID\|e1234 General/
FP /^GNLPID$/
FZ = 76
//

ID seqret-ncbiout-ref1
AP seqret
CL ../../data/testids.ncbi:REF_12345 test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>ref\|NP_007225\.1\|REF_12345 NCBI /
FP /^REFSEQ$/
FZ = 58
//

ID seqret-ncbiout-ref2
AP seqret
CL ../../data/testids.ncbi:NM_012488.1 test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>ref\|NM_012488\.1\| NCBI /
FP /^REFSEQ$/
FZ = 63
//

ID seqret-ncbiout-lcl
AP seqret
CL ../../data/testids.ncbi:LOCALID test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>lcl\|localid Local /
FP /^L-CALID$/
FZ = 57
//

ID seqret-ncbiout-gi
AP seqret
CL ../../data/testids.ncbi:123456 test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gi\|123456 gi prefix/
FP /^GIPREFIX$/
FZ = 30
//

ID seqret-ncbiout-gigb
AP seqret
CL ../../data/testids.ncbi:GIGENBANK test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gi\|123456\|gb\|G67890\|GIGENBANK gi /
FP /^GIGENBANK$/
FZ = 65
//

ID seqret-ncbiout-gisp
AP seqret
CL ../../data/testids.ncbi:GISWISS_PRT test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gi\|234567\|sp\|P01234\|GISWISS_PRT gi /
FP /^GISWISSPR-T$/
FZ = 71
//

ID seqret-ncbiout-gnlblast
AP seqret
CL ../../data/testids.ncbi:BLAST test.out -osf ncbi -auto
FI test.out
FP 1 /^>/
FP /^>gnl\|BL_ORD_ID\|0 Blast formatdb /
FP /^BLAST$/
FZ = 62
//

###############################################
# seqret (sequence input) associated qualifiers
###############################################

ID seq-end-fasta
AQ seqretsingle
CL tembl:v00294 -send 100 -out test.out -auto
FI test.out
FZ = 168
FP 1 /^>/
FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seq-begin-fasta
AQ seqretsingle
CL tembl:v00294 -sbegin 51 -send 100 -out test.out -auto
FI test.out
FZ = 117
FP 1 /^>/
FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seq-rev-fasta
AQ seqretsingle
CL tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -auto
FI test.out
FZ = 117
FP 1 /^>/
FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
//

ID seq-end-msf
AQ seqretsingle
CL tembl:v00294 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 395
FP 1 /^ +Name: /
FP  / +Name: V00294 .* Check: 8066/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seq-begin-msf
AQ seqretsingle
CL tembl:v00294 -sbegin 51 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 268
FP 1 / +Name: /
FP  / +Name: V00294 .* Check: 2937/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seq-rev-msf
AQ seqretsingle
CL tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -osf msf -auto
FI test.out
FZ = 268
FP 1 / +Name: /
FP  / +Name: V00294 .* Check: 9768/
FP /^V00294     ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
//

ID seqall-end-fasta
AP seqret
CL "tembl:v0029*" -send 100 -out test.out -auto
FI test.out
FZ = 517
FP 3 /^>/
FP /^ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca\n/
FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seqall-begin-fasta
AP seqret
CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -auto
FI test.out
FZ = 364
FP 3 /^>/
FP /^ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/
FP /^aaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcg\n/
//

ID seqall-rev-fasta
AP seqret
CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -auto
FI test.out
FZ = 364
FP 3 /^>/
FP /^atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/
FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
//

ID seqall-end-msf
AP seqret
CL "tembl:v0029*" -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 751
FP 3 / +Name: /
FP  / +Name: V00294 .* Check: 8066/
FP  / +Name: V00295 .* Check: 6545/
FP /^V00296     accatgattacggattcactggccgtcgttttacaacgtcgtgactggga\n/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seqall-begin-msf
AP seqret
CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 498
FP 3 / +Name: /
FP  / +Name: V00294 .* Check: 2937/
FP  / +Name: V00295 .* Check: 1564/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FP /^V00295     ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/
//

ID seqall-rev-msf
AP seqret
CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -osf msf -auto
FI test.out
FZ = 498
FP 3 / +Name: /
FP  / +Name: V00294 .* Check: 9768/
FP  / +Name: V00295 .* Check: 3152/
FP /^V00294     ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FP /^V00295     atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/
//

ID seqset-end-fasta
AQ seqretset
CL "tembl:v0029*" -send 100 -out test.out -auto
FI test.out
FZ = 517
FP 3 /^>/
FP /^ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca\n/
FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seqset-begin-fasta
AQ seqretset
CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -auto
FI test.out
FZ = 364
FP 3 /^>/
FP /^ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/
FP /^aaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcg\n/
//

ID seqset-rev-fasta
AQ seqretset
CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -auto
FI test.out
FZ = 364
FP 3 /^>/
FP /^atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/
FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
//

ID seqset-end-msf
AQ seqretset
CL "tembl:v0029*" -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 751
FP 3 / +Name: /
FP  / +Name: V00294 .* Check: 8066/
FP  / +Name: V00295 .* Check: 6545/
FP /^V00296     accatgattacggattcactggccgtcgttttacaacgtcgtgactggga\n/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
//

ID seqset-begin-msf
AQ seqretset
CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 498
FP 3 / +Name: /
FP  / +Name: V00294 .* Check: 2937/
FP  / +Name: V00295 .* Check: 1564/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FP /^V00295     ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/
//

ID seqset-rev-msf
AQ seqretset
CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -osf msf -auto
FI test.out
FZ = 498
FP 3 / +Name: /
FP  / +Name: V00294 .* Check: 9768/
FP  / +Name: V00295 .* Check: 3152/
FP /^V00294     ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FP /^V00295     atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/
//

######################################################
# end of seqret (sequence input) associated qualifiers
######################################################


###########################################################
# seqret (sequence and feature input) associated qualifiers
###########################################################

ID featseq-end-fasta
AQ seqretsingle
CL -feat tembl:v00294 -send 100 -out test.out -auto
FI test.out
FZ = 168
FP 1 /^>/
FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FC = 7
FZ = 1262
FP /^#!Type DNA\n/
FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true/
//

ID featseq-begin-fasta
AQ seqretsingle
CL -feat tembl:v00294 -sbegin 51 -send 100 -out test.out -auto
FI test.out
FP 1 /^>/
FZ = 117
FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 1294
FP /^##sequence-region V00294 1 50\n/
FP /^#!Type DNA\n/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseq-rev-fasta
AQ seqretsingle
CL -feat tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -auto
FI test.out
FZ = 117
FP 1 /^>/
FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FI test.gff
FZ = 1294
FP /^##sequence-region V00294 1 50\n/
FP /^#!Type DNA\n/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseq-end-embl
AQ seqretsingle
CL -feat tembl:v00294 -send 100 -out test.out -osf embl -auto
FI test.out
FZ = 2896
FP 1 /^ID   /
FP 1 /^FH   /
FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/
FP /^FT   CDS             31\.\.>100\n/
//

ID featseq-begin-embl
AQ seqretsingle
CL -feat tembl:v00294 -sbegin 51 -send 100 -out test.out -osf embl -auto
FI test.out
FZ = 2811
FP 1 /^ID   /
FP 1 /^FH   /
FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/
FP /^FT   CDS             <1\.\.>50\n/
//

ID featseq-rev-embl
AQ seqretsingle
CL -feat tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -osf embl -auto
FI test.out
FZ = 2835
FP 1 /^ID   /
FP 1 /^FH   /
FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/
FP /^FT   CDS             complement[(]<1\.\.>50[)]\n/
//

ID featseq-end-msf
AQ seqretsingle
CL -feat tembl:v00294 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 395
FP 1 /^ +Name: /
FP  / +Name: V00294 .* Check: 8066/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FC = 7
FZ = 1262
FP /^##sequence-region V00294 1 100\n/
FP /^#!Type DNA\n/
FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/
//

ID featseq-begin-msf
AQ seqretsingle
CL -feat tembl:v00294 -sbegin 51 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 268
FP 1 / +Name: /
FP  / +Name: V00294 .* Check: 2937/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 1294
FP /^##sequence-region V00294 1 50\n/
FP /^#!Type DNA\n/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseq-rev-msf
AQ seqretsingle
CL -feat tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -osf msf -auto
FI test.out
FZ = 268
FP 1 / +Name: /
FP  / +Name: V00294 .* Check: 9768/
FP /^V00294     ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FI test.gff
FZ = 1294
FP /^##sequence-region V00294 1 50\n/
FP /^#!Type DNA\n/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqall-end-fasta
AP seqret
CL -feat @../../data/eclac.list -send 100 -out test.out -auto
FI test.out
FZ = 877
FP 5 /^>/
FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8526
FP /^##sequence-region X51872 1 100\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/
//

ID featseqall-begin-fasta
AP seqret
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -auto
FI test.out
FZ = 622
FP 5 /^>/
FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8359
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqall-rev-fasta
AP seqret
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -auto
FI test.out
FZ = 622
FP 5 /^>/
FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/
FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FI test.gff
FZ = 8365
FP 5 /^#!Type DNA/
FP /^##sequence-region X51872 1 50\n/
FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqall-end-embl
AP seqret
CL -feat @../../data/eclac.list -send 100 -out test.out -osf embl -auto
FI test.out
FZ = 32134
FP 5 /^ID   /
FP 5 /^FH   /
FP /^ +caattcaggg tggtgaatgt gaaaccagta acgttatacg +100\n/
FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/
FP /^FT   CDS             31\.\.>100\n/
//

ID featseqall-begin-embl
AP seqret
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf embl -auto
FI test.out
FZ = 31364
FP 5 /^ID   /
FP 5 /^FH   /
FP /^ +ggaagagagt caattcaggg tggtgaatgt gaaaccagta acgttatacg +50/
FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/
FP /^FT   CDS             29\.\.>50\n/
FP /^FT   CDS             <1\.\.>50\n/
//

ID featseqall-rev-embl
AP seqret
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf embl -auto
FI test.out
FZ = 31508
FP 5 /^ID   /
FP 5 /^FH   /
FP /^ +cgtataacgt tactggtttc acattcacca ccctgaattg actctcttcc +50\n/
FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/
FP /^FT   CDS             complement[(]<1\.\.22[)]\n/
FP /^FT   CDS             complement[(]<1\.\.>50[)]\n/
//

ID featseqall-end-msf
AP seqret
CL -feat @../../data/eclac.list -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 1107
FP 5 / +Name: /
FP  / +Name: J01636 .* Check: 4203/
FP  / +Name: V00294 .* Check: 8066/
FP /^J01636     ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FP /^##sequence-region X51872 1 100\n/
FZ = 8526
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/
//

ID featseqall-begin-msf
AP seqret
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 728
FP 5 / +Name: /
FP  / +Name: J01636 .* Check: 1328/
FP  / +Name: V00294 .* Check: 2937/
FP /^J01636     ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8359
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqall-rev-msf
AP seqret
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf msf -auto
FI test.out
FZ = 728
FP 5 / +Name: /
FP  / +Name: J01636 .* Check: 2885/
FP  / +Name: V00294 .* Check: 9768/
FP /^J01636     cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/
FP /^V00294     ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FI test.gff
FZ = 8365
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqset-end-fasta
AQ seqretset
CL -feat @../../data/eclac.list -send 100 -out test.out -auto
FI test.out
FZ = 877
FP 5 /^>/
FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8526
FP /^##sequence-region X51872 1 100\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/
//

ID featseqset-begin-fasta
AQ seqretset
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -auto
FI test.out
FZ = 622
FP 5 /^>/
FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8359
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqset-rev-fasta
AQ seqretset
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -auto
FI test.out
FZ = 622
FP 5 /^>/
FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/
FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FI test.gff
FZ = 8365
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqset-end-embl
AQ seqretset
CL -feat @../../data/eclac.list -send 100 -out test.out -osf embl -auto
FI test.out
FZ = 32134
FP 5 /^ID   /
FP 5 /^FH   /
FP /^ +caattcaggg tggtgaatgt gaaaccagta acgttatacg +100\n/
FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/
FP /^FT   CDS             31\.\.>100\n/
//

ID featseqset-begin-embl
AQ seqretset
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf embl -auto
FI test.out
FZ = 31364
FP 5 /^ID   /
FP 5 /^FH   /
FP /^ +ggaagagagt caattcaggg tggtgaatgt gaaaccagta acgttatacg +50/
FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/
FP /^FT   CDS             29\.\.>50\n/
FP /^FT   CDS             <1\.\.>50\n/
//

ID featseqset-rev-embl
AQ seqretset
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf embl -auto
FI test.out
FZ = 31508
FP 5 /^ID   /
FP 5 /^FH   /
FP /^ +cgtataacgt tactggtttc acattcacca ccctgaattg actctcttcc +50\n/
FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/
FP /^FT   CDS             complement[(]<1\.\.22[)]\n/
FP /^FT   CDS             complement[(]<1\.\.>50[)]\n/
//

ID featseqset-end-msf
AQ seqretset
CL -feat @../../data/eclac.list -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 1107
FP 5 / +Name: /
FP  / +Name: J01636 .* Check: 4203/
FP  / +Name: V00294 .* Check: 8066/
FP /^J01636     ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8526
FP /^##sequence-region X51872 1 100\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/
//

ID featseqset-begin-msf
AQ seqretset
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf msf -auto
FI test.out
FZ = 728
FP 5 / +Name: /
FP  / +Name: J01636 .* Check: 1328/
FP  / +Name: V00294 .* Check: 2937/
FP /^J01636     ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/
FP /^V00294     cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/
FI test.gff
FZ = 8359
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

ID featseqset-rev-msf
AQ seqretset
CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf msf -auto
FI test.out
FZ = 728
FP 5 / +Name: /
FP  / +Name: J01636 .* Check: 2885/
FP  / +Name: V00294 .* Check: 9768/
FP /^J01636     cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/
FP /^V00294     ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/
FI test.gff
FZ = 8365
FP /^##sequence-region X51872 1 50\n/
FP 5 /^#!Type DNA/
FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/
FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/
//

##################################################################
# end of seqret (sequence and feature input) associated qualifiers
##################################################################

ID seqretsetall-ex
AP seqretsetall
CL -osf phylip
IN ../../data/globins-all.phy
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins-all.phylip
FZ = 3135
FP 1 /^ 7 164\n/
FP 1 /^ 7 167\n/
FP /^          FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE\n/
FP /^          FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF\n/
//

ID seqxref-ex
AP seqxref
CL tembl:x13776
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.seqxref
FC = 20
FP /^#tembl-id:X13776: 20\n/
FP 19 /[^:\s]+:[^:\s]+\n/
FP 3 /^UniProtKB/Swiss-Prot:/
FP 3 /^PDB:/
FP /^taxon:287\n/
//

ID seqxrefget-ex
AP seqxrefget
CL tembl:x13776
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.seqxrefget
FC = 20
FP /^#tembl-id:X13776: 20\n/
FP 19 /[^:\s]+:[^:\s]+\n/
FP 3 /^entret UniProtKB/Swiss-Prot:/
FP 3 /^textget PDB:/
FP /^taxtext taxon:287\n/
//

ID servertell-ex
AP servertell
CL srs
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 15
FP /^SERVER srs \[\n/
FP /^# databases: 16\n/
FP 1 /^   url:            "\S+"\n/
//

ID showalign-ex
AP showalign
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FZ = 2003
FP /^HBB_HUMAN  --------VH\.tPE\.K\.A\.TaL\.G\.V\.-VD\.\.\.\.E\.\.GR-\.LVvY\.WT\.R\.\.Es\.GD\.\.T\n/
FP /^Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx\n/
//

ID showalign-ex2
UC Show non-identities between the sequences
AP showalign
CL -show=n
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex3
UC Show all of the sequences
AP showalign
CL -show=a
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex4
UC Show identities between the sequences
AP showalign
CL -show=i
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex5
UC Show similarities between the sequences
AP showalign
CL -show=s
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex6
UC Show dissimilarities between the sequences
AP showalign
CL -show=d
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex7
UC Use the first sequence as the reference to compare to:
AP showalign
CL -ref=1
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex8
UC Show a range of sequences in uppercase, everything else in lowercase
AP showalign
CL -nocon -ref=1 -sl -upper 9-15 -nosimilarcase
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex9
UC Display the sequences in alphabetic order:
AP showalign
CL -order=a
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex10
UC Display the sequences in order of similarity to the reference sequence
AP showalign
CL -order=s
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex11
UC Format for HTML and highlight some interesting regions in different colours:
AP showalign
CL -html -high "4-13 green 43-43 red 51-56 blue"
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-colourfile
UC Format for HTML and highlight some interesting regions in different colours:
AP showalign
CL -html -high @../../data/showalign.colour
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-hashfile
UC Format for HTML and highlight some interesting regions in different colours:
AP showalign
CL -html -high @../../data/showalign.hashcolour
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showalign-ex12
UC No consensus line at the bottom
UC No ruler line
UC No numbers line
UC Don't repeat the reference sequence at the bottom of the sequences
UC Use sequence 1 as the reference sequence
UC Display residues from position 10 to 30 only 
AP showalign
CL -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30
IN ../../data/globins.msf
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.showalign
FP /HBB_HUMAN/
//

ID showdb-ex
UC Display information on the currently available databases:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^tsw\s+Protein,Protfeatures,Text/
FP /^tembl\s+Nucleotide,Refseq,Nucfeatures/
//

ID showdb-ex2
UC Write the results to a file:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -outfile showdb.out
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI showdb.out
FP /^tsw\s+Protein,Protfeatures,Text/
FP /^tembl\s+Nucleotide,Refseq,Nucfeatures/
//

ID showdb-ex3
UC Display information on one explicit database:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -database tsw
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^tsw\s+Protein,Protfeatures,Text/
FP 0 /^tembl/
//

ID showdb-ex4
UC Display information on the databases formatted in HTML:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -html
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^<tr><td>tsw</td><td>Protein Protfeatures Text</td>/
FP /^<tr><td>tembl</td><td>Nucleotide Refseq Nucfeatures</td>/
//

ID showdb-ex5
UC Display protein databases only:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -nonucleic
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^tsw\s+Protein,Protfeatures,Text/
FP 0 /^[^#]\S*\s+Nucleotide/
//

ID showdb-ex6
UC Display the information with no headings:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -noheading
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /\A\S+\s+[PN][a-z]+,[PN][a-z]+\s+/
FP 0 /\A#/
//

ID showdb-ex7
UC Display just a list of the available database names:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -noheading -notype -noid -noquery -noall -nocomment -auto
FI stdout
FP /^tsw\s+\n/
FP /^tembl\s+\n/
//

ID showdb-ex8
UC Display only the names and types:
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -only -type
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^tsw\s+Protein,Protfeatures,Text +\n/
FP /^tembl\s+Nucleotide,Refseq,Nucfeatures +\n/
//

ID showdb-ex9
UC Display everything
AP showdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
CL -full
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^tsw\s+Protein,Protfeatures,Text\s+OK\s+OK\s+OK\s+emblcd\s+1_all\s+6 id,acc,sv,des,org,key\s+0 -\s+1 hba_human\s+special\s+\S+\s+Swissprot native format with EMBL CD-ROM index\n/
//

ID showfeat-ex
AP showfeat
IN tembl:x65921
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.showfeat 
FZ = 1429
FP /\|=+\| 2016\n/
FP 5 /    mRNA\n/
FP /-> source\n/
//

ID showfeat-ex2
UC Display 'joined' features on one line with positions:
AP showfeat
CL -joinfeat -pos
IN tembl:x65921
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.showfeat 
FZ = 1150
FP /\|=+\| 2016\n/
FP /mRNA\n/
FP /source\n/
//

ID showfeat-ex3
UC Display just positions and names of CDS features - this can be used as a regions file in showseq:
AP showfeat
CL -typematch CDS -width 0 -noid -nodesc -noscale -pos 
IN tembl:x65921
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.showfeat 
FZ = 54
FP /CDS/
//

ID showorf-ex
AP showorf
IN tembl:x13776
IN
IN
FI stderr
FC = 10
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showorf
FZ = 22690
FP /^F1 +1 G  T  A  G  R  A  S  A  R  S  P  P  A  G  R  R  E  17\n/
FP /^R2 +106    Y  R  Q  G  L  M  Q  E  I  V  V  L  R  A  V  P  91\n/
//

ID showpep-ex
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 100
IN
IN
FI stderr
FC = 7
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep 
FZ = 1599
FP 1 /^\s+\|=+\|\n\s+polypeptide_domain note="/
FP 1 /^\s+\|=+\|\s+\|=+\|\n\s+DNA_contact note="/
FP 2 /^\s+\|\n\s+mutated_variant_site note="/
//

ID showpep-ex2
UC The standard list of output formats are only a small selection of the
UC possible ways in which a sequence might be displayed.  Precise control
UC over the output format is acheived by selecting the qualifier '-format 0' 
UC (Option 0 in the list of things to display).  For example,
UC by choosing format '0' and then specifying that we want to display the
UC things: 'b,t,s', we will output the sequence in the following way:
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 120
IN 0
IN b,t,s
IN 
FI stderr
FC = 14
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep 
FZ = 323
FP 2 /^          ----:----\|----:----\|----:----\|----:----\|----:----\|----:----\|\n/
FP /^          SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS/
//

ID showpep-ex3
UC Display only the sequence:
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep
FZ = 123
FP /^          MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ\n/
FP /^          SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE\n/
//

ID showpep-ex4
UC Protein sequence can be displayed in three-letter codes.
UC (The codes are displayed downwards, so the first code is 'Met'): 
AP showpep
CL tsw:rs24_takru -three -format 2
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI rs24_takru.showpep
FZ = 1296
FP /^          MAATVT/
//

ID showpep-ex5
UC Number the sequence lines in the margin: 
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep
FZ = 166
FP /^       61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 100\n/
//

ID showpep-ex6
UC Start the numbering at a specified value ('123' in this case):
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number -offset 123
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep 
FZ = 167
FP /^      183 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 222\n/
//

ID showpep-ex7
UC Make selected regions uppercase. (Use '-slower' to force the rest of
UC the sequence to be lowercase). 
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -slower -upper
CL "17-17,22-22"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep
FZ = 159
FP /          mkpvtlydvaeyagvsYqtvsRvvnqashvsaktrekveaamaelnyipnrvaqqlagkq\n/
FP /          slligvatsslalhapsqivaaiksradqlgasvvvsmve\n/
//

ID showpep-ex8
UC Add your own annotation to the display:
AP showpep
CL tsw:laci_ecoli -sbeg 1 -send 100 -format 2 -send 120
CL  -annotation "6-25 binding site 17-17 SNP 22-22 SNP"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI laci_ecoli.showpep
FZ = 2121
FP /binding site/
FP /^                          SNP  SNP\n/
//

ID showseq-ex
AP showseq
CL tembl:x13776 -sbeg 1 -send 100
IN
IN
FI stderr
FC = 12
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 729
FP 2 /^\s+\|=+\|\n\s+promoter note="/
//

ID showseq-ex2
UC The standard list of output formats are only a small selection of the
UC possible ways in which a sequence might be displayed.  Precise control
UC over the output format is acheived by selecting the qualifier '-format 0' 
UC (Option 0 in the list of things to display).  For example,
UC by choosing format '0' and then specifying that we want to display the
UC things: 'b,s,t,c', we will output the sequence in the following way:
AP showseq
CL tembl:x13776 -sbeg 1 -send 120
IN 0
IN b,s,t,c
IN 
FI stderr
FC = 28
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 511
FP /^          ggtacc/
//

ID showseq-ex3
UC Display only the sequence:
AP showseq
CL tembl:x13776 -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 123
FP /^          ggtacc/
FP /^          ctacctggcgagcctggagcacgagcgggttcgcttcgta\n/
//

ID showseq-ex4
UC Number the sequence lines in the margin: 
AP showseq
CL tembl:x13776 -sbeg 1 -send 100 -format 1 -number
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 212
FP /^        1 ggtacc/
//

ID showseq-ex5
UC Start the numbering at a specified value ('123' in this case):
AP showseq
CL tembl:x13776 -sbeg 1 -send 100 -format 1 -number -offset 123
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 213
FP /^      123 ggtacc/
//

ID showseq-ex6
UC Make selected regions uppercase.
UC (Use '-slower' to force the rest of the sequence to be lowercase). 
AP showseq
CL tembl:x13776 -sbeg 1 -send 100 -format 1 -slower
CL -upper "8-24,65-81"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 205
FP /^          ggtaccgCTGGCCGAGCATCTGCTcgatcaccaccagccgggcgacgggaactgcacgat\n/
FP /^          ctacCTGGCGAGCCTGGAGCAcgagcgggttcgcttcgta\n/
//

ID showseq-ex7
UC Translate selected regions: 
AP showseq
CL tembl:x13776 -sbeg 1 -send 120 -format 5 -trans 25-49,66-76
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 1221
FP /R  S  P  P  A  G  R  R  V/
FP /A  S  L/
//

ID showseq-ex8
UC Add your own annotation to the display:
AP showseq
CL tembl:x13776 -sbeg 1 -send 100 -format 2 -send 120 -annotation "13-26 binding site 15-15 SNP"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.showseq 
FZ = 919
FP /binding site/
//

ID showserver-ex
UC Display information on the currently available servers:
AP showserver
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 20
FP /^srs\s+text\s+Unknown\s+OK\s+OK\s+OK\s+16\s+\S+server\.srs/
//

ID shuffleseq-ex
UC This makes two randomised copies of the input sequence:
AP shuffleseq
CL -shuffle 2
IN tembl:L48662
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI l48662.fasta 
FZ = 950
FP 2 /^>L48662/
FP /^agccgg\n/
FP /^cctcgc\n/
//

# fix output file in example
ID sigcleave-ex
AP sigcleave
IN tsw:ach2_drome
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ach2_drome.sig
FP /^[(]1[)] Score 13\.739 length 13 at residues 29->41\n/
FP /^ Sequence: LLVLLLLCETVQA\n/
FP 9 /^ Sequence: /
//

ID sigcleave-multi
AP sigcleave
IN tsw:a*
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ach2_drome.sig
FP /^[(]1[)] Score 13\.739 length 13 at residues 29->41\n/
FP /^ Sequence: LLVLLLLCETVQA\n/
FP 28 /^ Sequence: /
FP 5 /^# No scores over 3\.50\n/
FP 17 /^# Reporting scores over 3\.50\n/
FP 17 /^# Sequence: /
//

ID silent-ex
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
AP silent
IN tembl:x65923
IN kpni
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.silent 
FC = 40
FP /^ +288 +293 +[+] +KpnI +GGTACC +291 +V\.V +Yes +T->A\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 2\n/
//

ID silent-seqs
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
AP silent
CL -sshow -tshow
IN tembl:x65923
IN kpni
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.silent 
FC = 60
FP /^ +288 +293 +[+] +KpnI +GGTACC +291 +V\.V +Yes +T->A\n/
FP /^\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 2\n/
//

ID silent-all
PP EMBOSS_DATA=../rebaseextract-keep/
PP export EMBOSS_DATA
AP silent
CL -allmut
IN tembl:x65923
IN kpni
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.silent 
FC = 42
FP /^ +288 +293 +[+] +KpnI +GGTACC +291 +V\.V +Yes +T->A\n/
FP /^ +27 +32 +[+] +KpnI +GGTACC +31 +A\.P +No +G->C\n/
FP /^\n/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 3\n/
//

ID sixpack-ex
AP sixpack
IN tembl:x13776
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.sixpack
FZ = 25376
FP /^          P  P  A  W  A  G  D  R  S  H  E  R  Q  L  A  A  R  Q  P  A     F1\n/
FP /^           R  Q  H  G  R  G  T  A  P  M  S  A  N  S  L  L  G  S  L  R    F2\n/
FP /^            A  S  M  G  G  G  P  L  P  [*]  A  P  T  R  C  S  A  A  C  A   F3\n/
FP /^     1261 ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg 1320\n/
FI x13776.fasta
FZ = 9445
FP /^>X13776_2_ORF4  Translation of X13776 in frame 2, ORF 4, threshold 1, 210aa\n/
FP /^PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP\n/
FP 67 /^>/
//

ID sixpack-mstart
AP sixpack
CL -mstart
IN tembl:x13776
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x13776.sixpack
FZ = 25376
FP /^          P  P  A  W  A  G  D  R  S  H  E  R  Q  L  A  A  R  Q  P  A     F1\n/
FP /^           R  Q  H  G  R  G  T  A  P  M  S  A  N  S  L  L  G  S  L  R    F2\n/
FP /^            A  S  M  G  G  G  P  L  P  [*]  A  P  T  R  C  S  A  A  C  A   F3\n/
FP /^     1261 ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg 1320\n/
FI x13776.fasta
FZ = 4506
FP /^>X13776_2_ORF2  Translation of X13776 in frame 2, ORF 2, threshold 1, 196aa\n/
FP /^MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI\n/
FP 30 /^>/
//

ID sirna-ex
AP sirna
IN tembl:x65923
IN 
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.sirna
FC = 114
FP /GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 85\n/
FI x65923.fasta
FC = 170
FP /aaaagtgagaggtcagactccta/
//

ID sirna-ex2
UC Show the first two bases of the 23 base target region in brackets.
UC These do not form part of the sequence to be ordered, but it is useful
UC to see if the 23 base region starts with an 'AA'.
AP sirna
CL -context
IN tembl:x65923
IN 
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.sirna
FC = 118
FP /\(AA\)GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 85\n/
FI x65923.fasta
FZ = 6120
FP /aaaagtgagaggtcagactccta/
//

ID sizeseq-ex
AP sizeseq
CL -osformat swiss
IN ../../data/globins.fasta
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.swiss
FC = 49
FP /\AID   HBA_HUMAN               Reviewed;         141 AA.\n/
//

ID skipredundant-ex
AP skipredundant
CL -threshold 80 -redundant ""
IN ../../data/globins.fasta
IN 
IN 
IN 
IN 
FI stderr
FC = 5
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI globins.keep
FC = 20
FP 5 /^>/
FI globins.redundant
FC = 8
FP 2 /^>/
//

ID skipseq-ex
UC This does not skip any sequences. It is exactly equivalent to seqret:
AP skipseq
IN @../../data/eclac.list
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.fasta
FZ = 15619
FP 5 /^>/
//

ID skipseq-ex2
UC This skips the first input sequence, writing out the others:
AP skipseq
CL -skip 1
IN @../../data/eclac.list
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.fasta
FZ = 7940
FP 4 /^>/
//

ID splitsource-ex
UC Split a sequence into original subsequences
AP splitsource
CL ena:A01139
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI a01139.fasta
FZ = 579
FP /\A>A01139_1_1-81/
FP /^>A01139_1_1-81 organism="Lactococcus lactis"/
FP /^>A01139_2_82-279 organism="Hirudo medicinalis"/
FP 2 /^>/
//
ID splitter-ex
UC Split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences:
AP splitter
CL tembl:BA000025 ba000025.split
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ba000025.split
FZ = 2287126
FP /\A>BA000025_1-10000/
FP /^>BA000025_10001-20000/
FP /^>BA000025_90001-100000/
FP 223 /^>/
//

ID splitter-ex2
UC Split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence:
AP splitter
CL tembl:BA000025 ba000025.split -size=50000 -over=3000
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ba000025.split
FZ = 2414678
FP /\A>BA000025_1-50000/
FP /^>BA000025_47001-97000/
FP 48 /^>/
//

# update example
ID stretcher-ex
AP stretcher
CL tsw:hba_human tsw:hbb_human
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.stretcher
FZ > 1442
FP /^# Matrix: EBLOSUM62\n/
FP /^# Gap_penalty: 12\n/
FP /^# Extend_penalty: 2\n/
FP /^# Identity: +65/149 \(43\.6%\)\n/
FP /^# Score: 277\n/
FP /^HBA_HU MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-D\n/
FP /^HBB_HU MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD\n/
//

ID stssearch-ex
AP stssearch
IN @../../data/eclac.list
IN ../../data/lac.primers
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.stssearch
FZ = 719
FP /^J01636: PrimA PrimerA matched at 532\n/
FP /^J01636: \(rev\) PrimA PrimerB matched at 689\n/
//

ID supermatcher-ex
TI 400
AP supermatcher
CL @../../data/eclac.list tembl:j01636 -word 50 
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI supermatcher.error
FZ = 0
FI j01636.supermatcher
FZ > 71230
FP /^J01636 +1 /
FP /^# Score: 37385\.0/
FP 5 /^# Score: /
FP /^X51872 +1801 [acgt]+ +1832\n/
//

ID supermatcher-range
TI 400
AP supermatcher
CL @../../data/eclac.list tembl:j01636 -word 50 -sbegin2 101 -send2 -101
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI supermatcher.error
FZ = 0
FI j01636.supermatcher
FZ > 69555
FP /^J01636 +101 /
FP /^# Score: 36385\.0/
FP 5 /^# Score: /
FP /^X51872 +1701 [acgt]+ +1732\n/
//

ID syco-ex
AP syco
CL -plot -cfile Epseae.cut
IN tembl:x13776
IN ps
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 16
FP /^Created syco\.ps\n/
FI syco.ps
FC = 971
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID taxget-ex
AP taxget
CL ttax:9606
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9606.tax
FP /^id: 9606\n/
FP 1 /^id: /
FP 3 /name: /
FP 1 /^parent: 9605\n/
FP 1 /^scientific name: Homo sapiens\n/
FC = 17
//

ID taxgetdown-ex
AP taxgetdown
CL ttax:9605 -oformat excel
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9605.excel
FP /^741158\t9605\tspecies\tY\tHomo sp. Altai\n/
FP 2 /\tHomo /
FC = 2
//

ID taxgetrank-ex
AP taxgetrank
CL ttax:9606 -oformat excel
IN
IN
FI stderr
FC = 31
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9606.excel
FP  /9604\t314295\tfamily\tN\tHominidae\n/
FP 1 /order/
FP 0 /\tY\t/
FC = 6
//

ID taxgetrank-ex2
AP taxgetrank
CL ttax:9606 -oformat excel
IN *
IN
FI stderr
FC = 31
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9606.excel
FP  /9604\t314295\tfamily\tN\tHominidae\n/
FP 4 /order/
FP 0 /\tY\t/
FC = 14
//

ID taxgetrank-ex3
AP taxgetrank
CL ttax:9606 -oformat excel -hidden
IN *
IN
FI stderr
FC = 31
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9606.excel
FP  /9604\t314295\tfamily\tN\tHominidae\n/
FP 5 /order/
FP /^314293\t376913\tinfraorder\tY\tSimiiformes\n/
FP 15 /\tY\t/
FC = 29
//

ID taxgetspecies-ex
AP taxgetspecies
CL taxon-tax:hominidae -oformat excel
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9604.excel
FP /^9606\t9605\tspecies\tY\tHomo sapiens\n/
FP 1 /\tHomo /
FP 4 /\tPongo /
FP 2 /\tGorilla /
FP 2 /\tPan /
FC = 9
//

ID taxgetup-ex
AP taxgetup
CL ttax:9606 -oformat excel
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9606.excel
FP 1 /^9605\t207598\tgenus\tN\tHomo\n/
FP 0 /^207598\t/
FC = 14
//

ID taxgetup-ex2
AP taxgetup
CL ttax:9606 -hidden -oformat excel
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI 9606.excel
FP 1 /^9605\t207598\tgenus\tN\tHomo\n/
FP 1 /^207598\t/
FC = 29
//

ID tcode-ex
AP tcode
IN tembl:x65921
IN 
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.tcode
FC = 635
FP /^      1     200       [+]   0\.617 Non-coding/
FP /^     22     221       [+]   0\.845 No opinion/
FP /^     37     236       [+]   0\.970 Coding/
//

ID tcode-ex2
UC Produce a graphical plot
CL -plot -graph cps
AP tcode
IN tembl:x65921
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 17
FP /^Created tcode\.ps\n/
FI tcode.ps
FC = 390
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID tcode-twoseqs
UC Produce a graphical plot
CL -plot -graph cps
AP tcode
IN tembl:{x65921,x13776}
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 17
FP /^Created tcode\.ps\n/
FI tcode.ps
FC = 706
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 2\n/
//

ID textget-ex
AP textget
CL "srs:unilib:99"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.text
FC = 37
FP /^> 99\n/
//

ID textsearch-ex
UC Search for 'lactose':
AP textsearch
CL "tsw:*" "lactose"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cru4_arath.textsearch
FZ = 167
FP /^tsw-id:LACI_ECOLI LACI_ECOLI    P03023\s+Lactose operon repressor/
FP /^tsw-id:LACY_ECOLI LACY_ECOLI    P02920\s+Lactose permease/
//

ID textsearch-ex2
UC Search for 'lactose' or 'permease' in E.coli proteins:
AP textsearch
CL "tsw:*_ecoli" "lactose | permease"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI bgal_ecoli.textsearch
FZ = 178
FP /^tsw-id:LACI_ECOLI LACI_ECOLI    P03023\s+Lactose operon repressor/
FP /^tsw-id:LACY_ECOLI LACY_ECOLI    P02920\s+Lactose permease/
//

# update example
ID textsearch-ex3
UC Output a search for 'lacz' formatted with HTML to a file:
AP textsearch
CL "tembl:*" "lacz" -html -outfile embl.lacz.html
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI embl.lacz.html
FZ = 351
FP /^<tr><td>tembl-id:J01636</td><td>J01636</td><td>J01636</td>\s+<td>E\.coli lactose operon with lacI, lacZ, lacY and lacA genes\.</td></tr>/
//

ID tfextract-keep
## Note: yeast is now fungi rather than plant.
DL keep
AP tfextract
PP EMBOSS_DATA=./
PP export EMBOSS_DATA
IN ../../data/site.dat
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 0
FI tffungi
FZ = 121
FP /^Y\$ADH1_02/
FI tfinsect
FZ = 0
FI tfvertebrate
FZ = 676
FC = 7
FP /^HS\$ALBU_01 +tGGTTAGtaattactaa R00077 T01951; HNF-1C;Quality: 1; Species: human, Homo sapiens\./
FP 5 /^HS\$ALBU/
FP 2 /^MOUSE/
FI tfplant
FZ = 0
FI tfother
FZ = 0
//

ID tfm-ex
AP tfm
CC wossname documentation subject to updates - will break file size test
CC On some systems 'more' also reports the filename at the start of the output
CL wossname
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ > 43000
FP 1 /^ +Find programs by keywords in their short description\n/
FP 1 /^ +-explode/
//

ID tfscan-ex
CC Needs tfextract to reformat TRANSFAC data
AP tfscan
PP EMBOSS_DATA=../tfextract-keep/
PP export EMBOSS_DATA
IN tembl:k00650
IN v
IN
IN
FI stderr
FC = 9
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI k00650.tfscan
FZ = 1614
FC = 34
FP /^   3287    3292       \+ R04413    T00702; .* Mus musculus\.      ttcctc\n/
//

ID tmap-ex
AP tmap
CL ../../data/opsd.msf -out tmap.res -graph cps
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 16
FP /^Created tmap\.ps\n/
FI tmap.res
FZ = 2337
FP 3 /^     43      70        1 YMF.*KLRT\n/
FP /^# Reported_sequences: 3\n/
FP /^# Reported_hitcount: 21\n/
FI tmap.ps
FC = 1409
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID tmap-single
AP tmap
CL tsw:opsd_human -out tmap.res -graph cps
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 16
FP /^Created tmap\.ps\n/
FI tmap.res
FZ = 1696
FP 2 /^     43      69        1 YMFLLIVLGFPINFLTLYVTVQHKKLR\n/
FP /^# Reported_sequences: 2\n/
FP /^# Reported_hitcount: 14\n/
FI tmap.ps
FC = 1426
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID tranalign-ex
AP tranalign
CL ../../data/tranalign.seq ../../data/tranalign.pep tranalign2.seq
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI tranalign2.seq
FZ = 2375
FP /^>HSFAU1/
FP /^cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg/
//

# update the examples
ID transeq-ex
UC To translate a sequence in the first frame (starting at the first base and proceeding to the end):
AP transeq
CL tembl:x13776 amir.pep
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 821
FP /^>X13776_1/
FP /^GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR\*SACCSP\n/
//

ID transeq-ex2
UC To translate a sequence in the second frame:
AP transeq
CL tembl:x13776 amir.pep -frame=2
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 820
FP /^>X13776_2/
FP /^VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR\*ATVTGEETDGIAPGAAADRPAVLR\n/
//

ID transeq-ex3
UC To translate a sequence in the first frame in the reverse sense (starting at the last frame 1 codon and proceeding to the start): 
AP transeq
CL tembl:x13776 amir.pep -frame=-1
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 820
FP /^>X13776_4/
FP /^SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS\*AIFRIGSRRFIAS\n/
//

ID transeq-ex4
UC To translate a sequence in all three forward frames:
AP transeq
CL tembl:x13776 amir.pep -frame=F
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 2461
FP /^>X13776_1/
FP /^>X13776_2/
FP /^>X13776_3/
FP /^CWARSAVGRWR\*STSWSAC\*APASRST\*SFPQQPGRAR\*RPER\*PCYSLLPICGWPPTSS\n/
//

ID transeq-ex5
UC To translate a sequence in all three reverse frames:
AP transeq
CL tembl:x13776 amir.pep -frame=R
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 2461
FP /^>X13776_4/
FP /^>X13776_5/
FP /^SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS\*AIFRIGSRRFIAS\n/
FP /^LEELVGGHPQIGKSE\*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA\n/
FP /^>X13776_6/
//

ID transeq-ex6
UC To translate a sequence in all six forward and reverse frames:
AP transeq
CL tembl:x13776 amir.pep -frame=6
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 4922
FP /^>X13776_1/
FP /^>X13776_2/
FP /^>X13776_3/
FP /^>X13776_4/
FP /^>X13776_5/
FP /^>X13776_6/
FP /^LEELVGGHPQIGKSE\*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA\n/
//

ID transeq-ex7
UC To translate a specific set of regions corresponding to a known set of coding sequences:
AP transeq
CL tembl:x13776 amir.pep -reg=2-45,67-201,328-509
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI amir.pep
FZ = 209
FP /^>X13776_1/
FP /^VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE\n/
FP /^X\Z/
//

ID transeq-ex8
UC To translate a mitochondrial sequence using the mammalian mitochondrion genetic code table:
AP transeq
CL ../../data/mito.seq mito.pep -table 2
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI mito.pep
FZ = 5626
FP /^>NC_001321\.1_1/
FP /^VNY\*SAHDHNMTEVSYIWYFFIFFGGLARTPLWP\*\*VSSQSDKL\*LGLDVFVIWLAQPTC\n/
//

ID transeq-list0
UC To translate from a list of sequences and test the ranges are set correctly
AP transeq
CL @../../data/range0.list list.pep
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI list.pep
FZ = 1237
FP /^LFSVVAAVPEIKMLLMTEKKKKKX\n/
FP /^STVTQLPTKWWPSRTSLLVRSSTPEETRPSRLTC\*PMAAASVPLSPAAHPLASTRRLSSV\n/
FP /^KKKKX\n/
//

ID transeq-list1
UC To translate from a list of sequences and test the ranges are set correctly
AP transeq
CL @../../data/range1.list list.pep
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI list.pep
FZ = 733
FP /^AAGKKLPR\n/
FP /^STVTQLPTKWWPSRTSLLVRSSTPEETRPSRLTC\*PMAAASVPLSPAAHPLASTRRLSSV\n/
FP /^KKKKX\n/
//

ID transeq-list2
UC To translate from a list of sequences and test the ranges are set correctly
AP transeq
CL @../../data/range2.list list.pep
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI list.pep
FZ = 1135
FP /^PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRR\n/
FP /^LFSVVAAVPEIKMLLMTEKKKKKX\n/
FP /^MVAIKDITARQILDSRGNPTVEVDLLTDGGCFRAAVPSGASTGIYEALELRDKDQTKFMG\n/
FP /^QLMRIEESLGSDCQYAGAGFRHPN\*\n/
//

ID transeq-list12
UC To translate from a list of sequences and test the ranges are set correctly
AP transeq
CL @../../data/range12.list list.pep
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI list.pep
FZ = 631
FP /^AAGKKLPR\n/
FP /^MVAIKDITARQILDSRGNPTVEVDLLTDGGCFRAAVPSGASTGIYEALELRDKDQTKFMG\n/
FP /^QLMRIEESLGSDCQYAGAGFRHPN\*\n/
//

ID trimest-ex
AP trimest
CL tembl:x65923 x65923.seq
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.seq
FZ = 575
FP /poly-A tail removed/
//

ID trimseq-ex
AP trimseq
CL ../../data/untrimmed.seq trim1.seq -window 1 -percent 100
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI trim1.seq
FZ = 528
FP /^>myseq/
FP /^ttyyyctttctcgactc/
FP /ttca-gnntcy\n/
//

ID trimseq-ex2
AP trimseq
CL ../../data/untrimmed.seq trim2.seq -window 5 -percent 40
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI trim2.seq
FZ = 523
FP /^>myseq/
FP /^ttyyyctttctcgactc/
FP /ttca-g\n/
//


ID trimseq-ex3
AP trimseq
CL ../../data/untrimmed.seq trim3.seq -window 5 -percent 50
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI trim3.seq
FZ = 528
FP /^>myseq/
FP /^ttyyyctttctcgactc/
FP /ttca-gnntcy\n/
//

ID trimseq-ex4
AP trimseq
CL ../../data/untrimmed.seq trim4.seq -window 5 -percent 50 -strict
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI trim4.seq
FZ = 522
FP /^>myseq/
FP /^ctttctcgactc/
FP /ttca-gnntc\n/
//

ID trimseq-ex5
AP trimseq
CL ../../data/untrimmed.seq trim5.seq -window 5 -percent 50 -strict -noright
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI trim5.seq
FZ = 529
FP /^>myseq/
FP /^ctttctcgactc/
FP /ttca-gnntcynnnnnn\n/
//

ID trimspace-ex
AP trimspace
IN ../../data/seqspace2.txt
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI seqspace2.trimspace
FC = 46
FP /^>X13776 Pseudomonas aeruginosa amiC and amiR gene\n/
FP /^ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga\n/
//

ID twofeat-ex
UC Without the -twoout option the output report contains just one feature
UC for every pair of features found.
AP twofeat
CL tembl:x65923
IN polyA_signal
IN polyA_site
IN 10
IN 50
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.twofeat
FZ = 842
FP /484     509       [+]   0\.000    484    489    509    509/
FP /^# Reported_sequences: 1\n/
FP /^# Reported_hitcount: 1\n/
//

ID twofeat-ex2
UC The -twoout option makes the output report give the pairs of features found. The output report format type has been changed to display the full original pairs of features in GFF format.
AP twofeat
CL -twoout -rformat gff tembl:x65923
IN polyA_signal
IN polyA_site
IN 10
IN 50
IN 
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65923.twofeat
FZ = 217
FP /polyA_signal_sequence\t484\t489/
//

ID urlget-ex
AP urlget
CL pseudocap:PA3363 -swiss
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pa3363.url
FC = 1
FP 1 /^http:\/\/www\.pseudomonas\.com\/getAnnotation\.do\?locusID\=PA3363        Locus ID \(PseudoCAP\): PA3363\n/
//

ID urlget-noswiss
AP urlget
CL pseudocap:PA3363
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pa3363.url
FC = 2
FP 1 /^http:\/\/www\.pseudomonas\.com\/getAnnotation\.do\?locusID\=PA3363        Locus ID \(PseudoCAP\): PA3363\n/
//

ID urlget-id
AP urlget
CL pseudocap:PA3363 -identifier "Locus ID (PseudoCAP)"
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI pa3363.url
FC = 1
FP 1 /^http:\/\/www\.pseudomonas\.com\/getAnnotation\.do\?locusID\=PA3363        Locus ID \(PseudoCAP\): PA3363\n/
//

ID union-ex
UC The file 'cds.list' contains a list of the regions making up the coding sequence of 'embl:x65923':
AP union
IN @../../data/cds.list
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x65921.fasta
FZ = 447
FP 1 /^>/
//


ID variationget-ex
AP variationget
CL ../../data/valid-4.0.vcf
IN test.vcf
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.vcf
FC = 34
FP /^##fileformat=VCFv4.0\n/
FP 21 /^##/
FP 1 /^#CHROM\t/
FP 12 /^[^#]/
//

ID variationget-v33
AP variationget
CL ../../data/valid-3.3.vcf
IN test.vcf
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.vcf
FC = 30
FP /^##fileformat=VCFv4.0\n/
FP 19 /^##/
FP 1 /^#CHROM\t/
FP 10 /^[^#]/
//

ID variationget-v40
AP variationget
CL ../../data/valid-4.0.vcf
IN test.vcf
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.vcf
FC = 34
FP /^##fileformat=VCFv4.0\n/
FP 21 /^##/
FP 1 /^#CHROM\t/
FP 12 /^[^#]/
//

ID variationget-v41
AP variationget
CL ../../data/valid-4.1.vcf
IN test.vcf
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.vcf
FC = 37
FP /^##fileformat=VCFv4.0\n/
FP 25 /^##/
FP 1 /^#CHROM\t/
FP 11 /^[^#]/
//

ID vectorstrip-ex
AP vectorstrip
CL @../../data/vecseqs.list
IN
IN ../../data/vectors
IN
IN
IN vector.strip
IN vector.fasta
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI vector.strip
FZ = 1835
FP /tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca/
FI vector.fasta
FZ = 457
FP /tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca/
//

ID water-ex
AP water
CL tsw:hba_human tsw:hbb_human
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.water 
FZ > 1175
FP /^# Score: 293\.5\n/
FP /^HBA_HUMAN +3 +LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS- +50\n/
FP /^HBB_HUMAN +4 +LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST +51\n/
FP /^HBA_HUMAN +51 +----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP +96\n/
FP /^# Identity: +63/145 \(43\.4%\)\n/
FP /^# Similarity: +88/145 \(60\.7%\)\n/
//

ID water-gapafterfirstresidue
AP water
CL asis:catt asis:cgatt stdout -auto -gapopen 1 -gapextend 1
FI stdout 
FZ > 15
FP /# Score: 19/
FP /.*c-att/
FP /.*cgatt/
//

ID whichdb-ex
AP whichdb
PP EMBOSS_RCHOME=N
PP export EMBOSS_RCHOME
TI 300
CL -showall
IN x65923
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI outfile.whichdb
FZ > 0
FP /^tembl:x65923\n/
FP 19 /^[a-z0-9]+:x65923\n/
//

ID wobble-ex
UC Here is a sample session with wobble. The example sequence is from
UC Pseudomonas aeruginosa, which has a high G+C content and a very biased
UC third codon position (if it can be G or C, it usually is).
AP wobble
IN tembl:x13776
IN cps
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 18
FP /^Created wobble\.ps\n/
FI x13776.wobble
FZ = 46
FP /^Expected GC content in third position = 66\.54\n/
FI wobble.ps
FC = 1749
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID wordcount-ex
AP wordcount
CL tembl:u68037 -wordsize=3
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI u68037.wordcount
FZ = 432
FP /\Actg\s+54\n/
FP /^aaa\s+1\Z/
//

ID wordfinder-ex
TI 400
AP wordfinder
CL tembl:j01636 @../../data/eclac.list -word 50 
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI wordfinder.error
FC = 5
FP 5 /^Target [0-9]+ [A-Z][0-9]+ matches 1\n/
FI j01636.wordfinder
FZ > 71230
FP /^J01636 +1 /
FP /^# Score: 37385\.0/
FP 5 /^# Score: /
FP /^X51872 +1801 [acgt]+ +1832\n/
//

ID wordmatch-ex
AP wordmatch
CL tsw:hba_human tsw:hbb_human
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP /^ +5 HBA_HUMAN +[+] +59\.\.63 +HBB_HUMAN +[+] +64\.\.68\n/
FP /^ +4 HBA_HUMAN +[+] +15\.\.18 +HBB_HUMAN +[+] +16\.\.19\n/
FP /^ +4 HBA_HUMAN +[+] +117\.\.120 +HBB_HUMAN +[+] +122\.\.125\n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /Number of patterns\/words found: 139/
//

ID wossdata-ex
UC Search for programs with 'codon' in their input, output or parameters
AP wossdata
CL codon
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 10 /^[a-z]\S+ /
FP /^cai /
FP /^chips /
FP /^cusp /
FP /^cutgextract /
FP 0 /seqret /
FC = 12
//

ID wossinput-ex
UC Search for programs with 'codon' in their input:
AP wossinput
CL codon
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 8 /^[a-z]\S+ /
FP /^cai /
FP /^cutgextract /
FP 0 /^chips /
FP 0 /^cusp /
FP 0 /seqret /
FC = 10
//

ID wossname-ex
UC Search for programs with 'restrict' in their description:
AP wossname
CL restrict
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^recoder /
FP /^remap /
FP /^restover /
FP /^silent /
FP 0 /seqret /
//

ID wossname-ex2
UC Display a listing of programs in their groups:
AP wossname
CL -search ""
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^recoder /
FP /^remap /
FP /^restover /
FP /^silent /
FP /^seqret /
FP /^DATA RESOURCES/
//

ID wossname-ex3
UC Display an alphabetic listing of all programs:
AP wossname
CL -search "" -alphabetic
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP s /\AALPHABETIC.*\naaindexextract /
//

ID wossname-ex4
UC Display only the groups that the programs can belong to:
AP wossname
CL -search "" -groups
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^[A-Z]/
FP 0 /^[^A-Z]/
//

ID wossname-ex5
UC Output html tags around the list of programs:
AP wossname
CL "" -html -out wossname.html
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI wossname.html
FP /<a href="abiview\.html"/
FP /<a href="[\/\\]embassy[\/\\]mse[\/\\]mse\.html"/
//

ID wossoperation-ex
UC Search for programs with 'codon' in their operation:
AP wossoperation
CL codon
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 7 /^[a-z]\S+ /
FP /^cai /
FP /^chips /
FP /^cusp /
FP 0 /^cutgextract /
FP 0 /seqret /
FC = 9
//

ID wossoutput-ex
UC Search for programs with 'codon' in their output:
AP wossoutput
CL codon
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 6 /^[a-z]\S+ /
FP /^cai /
FP /^chips /
FP /^cusp /
FP 0 /^cutgextract /
FP 0 /seqret /
FC = 8
//

ID wossparam-ex
UC Search for programs with 'codon' in their parameters:
AP wossparam
CL codon
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^[a-z]\S+ /
FP /^syco /
FP 0 /^cusp /
FP 0 /^cutgextract /
FP 0 /seqret /
FC = 3
//

ID wosstopic-ex
UC Search for programs with 'codon' in their topic:
AP wosstopic
CL codon
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 7 /^[a-z]\S+ /
FP /^cai /
FP /^chips /
FP /^cusp /
FP /^cutgextract /
FP /^syco /
FP 0 /seqret /
FC = 9
//

ID xmlget-ex
AP xmlget
CL dbfetch:embl:x13776
IN
FI x13776.xml
FC = 277
FP 1 /^<ROOT/
FP 3 /^\s+<keyword>[^<>]+<\/keyword>\n/
FP 4 /^\s+<reference type=/
FP 10 /^\s+<feature name=/
FP 7 /^\s+<taxon scientificName=/
FP 25 /^\s+<qualifier name=/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID xmltext-ex
AP xmltext
CL dbfetch:embl:x13776
IN
FI x13776.xmltext
FC = 278
FP 1 /^<ROOT/
FP 3 /^\s+<keyword>[^<>]+<\/keyword>\n/
FP 4 /^\s+<reference type=/
FP 10 /^\s+<feature name=/
FP 7 /^\s+<taxon scientificName=/
FP 25 /^\s+<qualifier name=/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID yank-ex
UC This is an example of adding an entry for the part of tembl:x65921 between positions 1913 and 1915 to the existing list file 'cds.list':
AP yank
PP cp ../../data/cds.list .
IN tembl:x65921
IN 1913
IN 1915
IN
IN cds.list
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI cds.list
FZ = 132
FC = 5
FP 5 /tembl-id:X65921\[[0-9]+:[0-9]+\]\n/
//

###########################################################
# Checking alignment reports
# with sbegin, send, various formats, and
# different internal alignment functions
#
# Functions              Programs         Comments
#
# seqmatchall program    seqmatchall      Pair Global
# stretcher   program    stretcher        Pair Global
# matcher     program    matcher          Pair Local
# wordmatch   program    wordmatch        Pair Local Ungapped
#
# embAlignReportGlobal   merger           Pair Global
#                        needle           Pair Global
# embAlignReportLocal    water            Pair Local
#                        supermatcher     Pair Local
###########################################################

ID align-seqmatchall-default
## Using an increased word size to avoid accidental matches:
AP seqmatchall
IN @../../data/eclac.list
IN 15
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.seqmatchall
FZ = 1623
FP /^  1832 J01636 +[+] +5646\.\.7477     X51872 +[+] +1\.\.1832\n/
FP /^  1113 J01636 +[+] +49\.\.1161     V00294 +[+] +1\.\.1113\n/
FP /^  1500 J01636 +[+] +4305\.\.5804     V00295 +[+] +1\.\.1500\n/
FP /^  3078 J01636 +[+] +1287\.\.4364     V00296 +[+] +1\.\.3078\n/
FP /^   159 X51872 +[+] +1\.\.159      V00295 +[+] +1342\.\.1500\n/
FP /^    60 V00295 +[+] +1\.\.60       V00296 +[+] +3019\.\.3078\n/
//

ID align-stretcher-msfgap
AP stretcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin2 4
CL -aformat msf
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^AFULL +GGCCAATTGGCATG\n/
FP 1 /^BFULL +~{17}CGGG\.{9}CC\.{14}TTT~\n/
FC = 17
//

ID align-stretcher-full
AP stretcher
CL -gapopen 16 -gapextend 1 -stdout
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/64 \(15\.6%\)/
FP /^# Score: +-55\n/
FP 1 /^               10        20        30        40        50\n/
FP 1 /^ AFULL ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTTCCCAAATTTG\n/
FP 1 /^ BFULL A------------AAC----------------GGGCCTTT----------\n/
FP 1 /^                                           10            \n/
FC = 46
//

ID align-stretcher-part
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +47\/65 \(72\.3%\)/
FP /^# Score: +115\n/
FP 1 /^                60    \n/
FP 1 /^ AFULL GGCC-AATTGGCATG\n/
FP 1 /^ APART GGTTTAACCGG--TT\n/
FP 1 /^            50        \n/
FC = 46
//

ID align-stretcher-begin
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -sbegin1 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/60 \(13\.3%\)/
FP /^# Score: +-180\n/
FP 1 /^           10        20        30        40        50    \n/
FP 1 /^ AFULL AACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTTCCCAAATTTGGGCC\n/
FP 1 /^       :: :::                                            \n/
FP 1 /^ BFULL AAACGG--------------------------------------------\n/
FP 1 /^           60    \n/
FP 1 /^ AFULL AATTGGCATG\n/
FP 1 /^           : : : \n/
FP 1 /^ BFULL ----GCCTTT\n/
FP 1 /^             10  \n/
FC = 47
//

ID align-stretcher-end
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -send1 15
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/15 \(40\.0%\)/
FP /^# Score: +-18\n/
FP 1 /^               10     \n/
FP 1 /^ AFULL ACGTAACCGGTTAAA\n/
FP 1 /^ BFULL A---AACGGGCCTTT\n/
FP 1 /^                  10  \n/
FC = 41
//

ID align-stretcher-begin2
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -sbegin2 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/64 \( 9\.4%\)/
FP /^# Score: +-226\n/
FP 1 /^               10        20        30        40        50\n/
FP 1 /^ AFULL ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTTCCCAAATTTG\n/
FP 1 /^ BFULL --------------------------------GGGCCTTT----------\n/
FP 1 /^                                           10            \n/
FC = 47
//

ID align-stretcher-end2
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -send2 -3
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +9\/64 \(14\.1%\)/
FP /^# Score: +-211\n/
FP 1 /^               60    \n/
FP 1 /^ AFULL GGCCAATTGGCATG\n/
FP 1 /^ BFULL GGCCT---------\n/
FP 1 /^          10         \n/
FC = 47
//

ID align-stretcher-begendall
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/11 \(45\.5%\)/
FP /^# Score: +-11\n/
FP 1 /^           10     \n/
FP 1 /^ AFULL AACCGGTTAAA\n/
FP 1 /^ BFULL AACGGG-----\n/
FP 1 /^            7     \n/
FC = 44
//

ID align-stretcher-fullrev
AP stretcher
CL -gapopen 16 -gapextend 1 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/64 \(15\.6%\)/
FP /^# Score: +-55\n/
FP 1 /^          60        50        40        30        20     \n/
FP 1 /^ AFULL CATGCCAATTGGCCCAAATTTGGGAAAACCCCGGGGTTTTAAACCCGGGT\n/
FP 1 /^ BFULL ------------------------AAAGGCCC----------------GT\n/
FP 1 /^          10         \n/
FC = 48
//

ID align-stretcher-partrev
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +47\/65 \(72\.3%\)/
FP /^# Score: +115\n/
FP 1 /^           10         \n/
FP 1 /^ AFULL TTTAACCGGTTACGT\n/
FP 1 /^ APART TTTAACCGGTT----\n/
FP 1 /^       10             \n/
FC = 48
//

ID align-stretcher-beginrev
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -sbegin1 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/60 \(13\.3%\)/
FP /^# Score: +-180\n/
FP 1 /^          60        50        40        30        20     \n/
FP 1 /^ AFULL CATGCCAATTGGCCCAAATTTGGGAAAACCCCGGGGTTTTAAACCCGGGT\n/
FP 1 /^ BFULL AAAGGC--------------------------------------------\n/
FP 1 /^        10                                               \n/
FP 1 /^          10     \n/
FP 1 /^ AFULL TTAACCGGTT\n/
FP 1 /^ BFULL ----CCGTTT\n/
FC = 49
//

ID align-stretcher-endrev
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -send1 15 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/15 \(40\.0%\)/
FP /^# Score: +-18\n/
FP 1 /^           10         \n/
FP 1 /^ AFULL TTTAACCGGTTACGT\n/
FP 1 /^ BFULL AAAGGCCCGTT---T\n/
FP 1 /^        10            \n/
FC = 43
//

ID align-stretcher-begin2rev
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -sbegin2 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/64 \( 9\.4%\)/
FP /^# Score: +-226\n/
FP 1 /^          60        50        40        30        20     \n/
FP 1 /^ AFULL CATGCCAATTGGCCCAAATTTGGGAAAACCCCGGGGTTTTAAACCCGGGT\n/
FP 1 /^ BFULL ------------------------AAAGGCCC------------------\n/
FP 1 /^                                10                       \n/
FC = 49
//

ID align-stretcher-end2rev
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -send2 -3 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +9\/64 \(14\.1%\)/
FP /^# Score: +-211\n/
FP /^          10         \n/
FP /^ AFULL TTAACCGGTTACGT\n/
FP /^ BFULL TT------------\n/
FP /^                     \n/
FC = 49
//

ID align-stretcher-begendallrev
AP stretcher
CL -gapopen 16 -gapextend 4 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/11 \(45\.5%\)/
FP /^# Score: +-11\n/
FP /^           10     \n/
FP /^ AFULL TTTAACCGGTT\n/
FP /^ BFULL -----CCCGTT\n/
FP /^                 2\n/
FC = 46
//

ID align-matcher-full
AP matcher
CL -gapopen 5 -gapextend 1 -stdout
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\n/
FP 1 /^                 10  \n/
FP 1 /^             20      \n/
FP 1 /^ AFULL AAACCCGGG--TTT\n/
FP 1 /^ BFULL AAAC--GGGCCTTT\n/
FC = 40
//


ID align-matcher-long
AP matcher
CL -gapopen 5 -gapextend 1 -stdout
IN tembl:j01636
IN tembl:v00296
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +3078\/3078 \(100\.0%\)/
FP /^# Score: +15390\n/
FP 1 /^       4340      4350      4360    \n/
FP 1 /^             3060      3070        \n/
FP 2 /^ *\S+ +GTTGGTCTGGTGTCAAAAATAATAATAA\n/
FC = 406
//


ID align-matcher-longrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2
IN tembl:j01636
IN tembl:v00296
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +3078\/3078 \(100\.0%\)/
FP /^# Score: +15390\n/
FP 1 /^        1310      1300      1290   \n/
FP 1 /^              20        10         \n/
FP 2 /^ *\S+ +CGACGGCCAGTGAATCCGTAATCATGGT\n/
FC = 408
//


ID align-matcher-part
AP matcher
CL -gapopen 5 -gapextend 1 -stdout
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +46\/64 \(71\.9%\)/
FP /^# Score: +196\n/
FP 1 /^ AFULL T----GGGCCAATT\n/
FP 1 /^ APART TAACCGG-----TT\n/
FP 1 /^        50           \n\n/
FP 1 /^           10        20        30        40              \n/
FP 1 /^               10        20        30           40       \n/
FC = 46
//

ID align-matcher-begin
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\n/
FP 1 /^             20      \n/
FP 1 /^ AFULL AAACCCGGG--TTT\n/
FP 1 /^ BFULL AAAC--GGGCCTTT\n/
FP 1 /^                 10  \n/
FC = 41
//

ID align-matcher-end
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -send1 15
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/10 \(70\.0%\)/
FP /^# Score: +25\n/
FP 1 /^           10    \n/
FP 1 /^ AFULL AACCGG--TT\n/
FP 1 /^ BFULL AACGGGCCTT\n/
FP 1 /^              10 \n/
FC = 41
//

ID align-matcher-begin2
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin2 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/9 \(77\.8%\)/
FP /^# Score: +29\n/
FP 1 /^      50        \n/
FP 1 /^ AFULL GGGCCAATT\n/
FP 1 /^ BFULL GGGCC--TT\n/
FP 1 /^             10 \n/
FC = 41
//

ID align-matcher-end2
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -send2 -3
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/11 \(72\.7%\)/
FP /^# Score: +30\n/
FP 1 /^            50    \n/
FP 1 /^ AFULL AAATTTGGGCC\n/
FP 1 /^ BFULL AAA--CGGGCC\n/
FP 1 /^                 9\n/
FC = 41
//

ID align-matcher-begendall
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^           10\n/
FP 1 /^ AFULL AACCGG\n/
FP 1 /^ BFULL AACGGG\n/
FP 1 /^            7\n/
FC = 44
//

ID align-matcher-pair
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat pair
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^AFULL +5 AACCGG +10\n/
FP 1 /^BFULL +2 AACGGG +7\n/
FC = 43
//

ID align-matcher-srspair
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat srspair
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^AFULL +5 AACCGG +10\n/
FP 1 /^BFULL +2 AACGGG +7\n/
FC = 43
//

ID align-matcher-markx0
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat markx0
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^           10\n/
FP 1 /^ AFULL AACCGG\n/
FP 1 /^       ::: ::\n/
FP 1 /^ BFULL AACGGG\n/
FP 1 /^            7\n/
FC = 45
//

ID align-matcher-markx1
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat markx1
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^           10\n/
FP 1 /^ AFULL AACCGG\n/
FP 1 /^          X  \n/
FP 1 /^ BFULL AACGGG\n/
FP 1 /^            7\n/
FC = 45
//

ID align-matcher-markx2
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat markx2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^           10\n/
FP 1 /^ AFULL AACCGG\n/
FP 1 /^ BFULL \.\.\.G\.\.\n/
FC = 43
//

ID align-matcher-markx3
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat markx3
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^>AFULL \.\.\nAACCGG\n/
FP 1 /^>BFULL \.\.\nAACGGG\n/
FC = 43
//

ID align-matcher-markx10
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat markx10
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^>AFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nAACCGG\n/
FP 1 /^>BFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nAACGGG\n/
FC = 64
//

ID align-matcher-fasta
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat fasta
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^>AFULL\n/
FP 1 /^AACCGG\n/
FP 1 /^>BFULL\n/
FP 1 /^AACGGG\n/
FC = 4
//

ID align-matcher-msf
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -aformat msf
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^AFULL +AACCGG\n/
FP 1 /^BFULL +AACGGG\n/
FC = 13
//

ID align-matcher-msfall
AP matcher
CL -gapopen 5 -gapextend 1 -stdout
CL -aformat msf
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^AFULL +AAACCCGGG\.\.TTT\n/
FP 1 /^BFULL +AAAC\.\.GGGCCTTT\n/
FC = 13
//

ID align-matcher-fullrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\n/
FP 1 /^            20       \n/
FP 1 /^ AFULL AAA--CCCGGGTTT\n/
FP 1 /^ BFULL AAAGGCCCG--TTT\n/
FP 1 /^        10           \n/
FC = 42
//


ID align-matcher-partrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +46\/64 \(71\.9%\)/
FP /^# Score: +196\n/
FP 1 /^                  50              40        30        20 \n/
FP 1 /^            50             40           30        20     \n/
FP 1 /^              10     \n/
FP 1 /^ AFULL GGGTTTAACCGGTT\n/
FP 1 /^ APART GGGTTTAACCGGTT\n/
FP 1 /^          10         \n/
FC = 48
//

ID align-matcher-beginrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\n/
FP 1 /^            20       \n/
FP 1 /^ AFULL AAA--CCCGGGTTT\n/
FP 1 /^ BFULL AAAGGCCCG--TTT\n/
FP 1 /^        10           \n/
FC = 43
//

ID align-matcher-endrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -send1 15 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/10 \(70\.0%\)/
FP /^# Score: +25\n/
FP 1 /^          10     \n/
FP 1 /^ AFULL AA--CCGGTT\n/
FP 1 /^ BFULL AAGGCCCGTT\n/
FP 1 /^       10        \n/
FC = 43
//

ID align-matcher-begin2rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin2 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/9 \(77\.8%\)/
FP /^# Score: +29\n/
FP 1 /^              50\n/
FP 1 /^ AFULL AATTGGCCC\n/
FP 1 /^ BFULL AA--GGCCC\n/
FP 1 /^       10       \n/
FC = 43
//

ID align-matcher-end2rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -send2 -3 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/11 \(72\.7%\)/
FP /^# Score: +30\n/
FP /^          50      \n/
FP /^ AFULL GGCCCAAATTT\n/
FP /^ BFULL GGCCCG--TTT\n/
FP /^                 1\n/
FC = 43
//

ID align-matcher-begendallrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP /^      10     \n/
FP /^ AFULL CCGGTT\n/
FP /^ BFULL CCCGTT\n/
FP /^            2\n/
FC = 46
//

ID align-matcher-pairrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat pair
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^AFULL +10 CCGGTT +5\n/
FP 1 /^BFULL +7 CCCGTT +2\n/
FC = 45
//

ID align-matcher-srspairrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat srspair
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^AFULL +10 CCGGTT +5\n/
FP 1 /^BFULL +7 CCCGTT +2\n/
FC = 45
//

ID align-matcher-markx0rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat markx0
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^      10     \n/
FP 1 /^ AFULL CCGGTT\n/
FP 1 /^       :: :::\n/
FP 1 /^ BFULL CCCGTT\n/
FP 1 /^            2\n/
FC = 47
//

ID align-matcher-markx1rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat markx1
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^      10     \n/
FP 1 /^ AFULL CCGGTT\n/
FP 1 /^         X   \n/
FP 1 /^ BFULL CCCGTT\n/
FP 1 /^            2\n/
FC = 47
//
ID align-matcher-markx2rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat markx2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^      10     \n/
FP 1 /^ AFULL CCGGTT\n/
FP 1 /^ BFULL \.\.C\.\.\.\n/
FC = 45
//

ID align-matcher-markx3rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat markx3
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\n/
FP 1 /^>AFULL \.\.\nCCGGTT\n/
FP 1 /^>BFULL \.\.\nCCCGTT\n/
FC = 45
//

ID align-matcher-markx10rev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat markx10
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^>AFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nCCGGTT\n/
FP 1 /^>BFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nCCCGTT\n/
FC = 66
//

ID align-matcher-fastarev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat fasta
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^>AFULL\n/
FP 1 /^CCGGTT\n/
FP 1 /^>BFULL\n/
FP 1 /^CCCGTT\n/
FC = 4
//

ID align-matcher-msfrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
CL -aformat msf
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^AFULL +CCGGTT\n/
FP 1 /^BFULL +CCCGTT\n/
FC = 13
//

ID align-matcher-msfallrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2
CL -aformat msf
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP 1 /^AFULL +AAA\.\.CCCGGGTTT\n/
FP 1 /^BFULL +AAAGGCCCG\.\.TTT\n/
FC = 13
//

ID align-matcherprot-full
AP matcher
CL -stdout
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +40\/68 \(58\.8%\)/
FP /^# Score: +198\n/
FP 1 /^             60        70\n/
FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/
FP 1 /^       ::::::: \. :::::\.:\.\n/
FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/
FP 1 /^               60        \n/
FC = 44
//


ID align-matcherprot-begin
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +40\/68 \(58\.8%\)/
FP /^# Score: +195\n/
FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/
FP 1 /^       ::::::: \. :::::\.:\.\n/
FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/
FP 1 /^               60        \n/
FC = 47
//

ID align-matcherprot-end
AP matcher
CL -stdout -send1 15
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/13 \(61\.5%\)/
FP /^# Score: +42\n/
FP 1 /^             10     \n/
FP 1 /^ AFULL FIAAEEFLFIIAA\n/
FP 1 /^       ::::\.\.:  \.:::\n/
FP 1 /^ BFULL FIAADDFFILIAA\n/
FP 1 /^               10   \n/
FC = 39
//

ID align-matcherprot-begin2
AP matcher
CL -stdout -sbegin2 5
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +36\/64 \(56\.[23]%\)/
FP /^# Score: +180\n/
FP 1 /^ AFULL IAALEEFFIIAEFL\n/
FP 1 /^       ::: \. :::::\.:\.\n/
FP 1 /^ BFULL IAADDLFFIIADFI\n/
FP 1 /^           60        \n/
FC = 45
//

ID align-matcherprot-end2
AP matcher
CL -stdout -send2 -3
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +40\/68 \(58\.8%\)/
FP /^# Score: +198\n/
FP 1 /^             60        70\n/
FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/
FP 1 /^       ::::::: \. :::::\.:\.\n/
FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/
FP 1 /^               60        \n/
FC = 45
//

ID align-matcherprot-begendall
AP matcher
CL -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/11 \(54\.5%\)/
FP /^# Score: +32\n/
FP 1 /^           10     \n/
FP 1 /^ AFULL AAEEFLFIIAA\n/
FP 1 /^ BFULL AADDFFILIAA\n/
FP 1 /^             10   \n/
FC = 42
//

ID align-matcherprot-fullrev
AP matcher
CL -stdout -srev1 -srev2
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +40\/68 \(58\.8%\)/
FP /^# Score: +198\n/
FP 1 /^             60        70\n/
FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/
FP 1 /^       ::::::: \. :::::\.:\.\n/
FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/
FP 1 /^               60        \n/
FC = 46
//


ID align-matcherprot-beginrev
AP matcher
CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -srev1 -srev2
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +40\/68 \(58\.8%\)/
FP /^# Score: +195\n/
FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/
FP 1 /^       ::::::: \. :::::\.:\.\n/
FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/
FP 1 /^               60        \n/
FC = 49
//

ID align-matcherprot-endrev
AP matcher
CL -stdout -send1 15 -srev1 -srev2
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/13 \(61\.5%\)/
FP /^# Score: +42\n/
FP 1 /^             10     \n/
FP 1 /^ AFULL FIAAEEFLFIIAA\n/
FP 1 /^       ::::\.\.:  \.:::\n/
FP 1 /^ BFULL FIAADDFFILIAA\n/
FP 1 /^               10   \n/
FC = 41
//

ID align-matcherprot-begin2rev
AP matcher
CL -stdout -sbegin2 5 -srev1 -srev2
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +36\/64 \(56\.[23]%\)/
FP /^# Score: +180\n/
FP 1 /^ AFULL IAALEEFFIIAEFL\n/
FP 1 /^       ::: \. :::::\.:\.\n/
FP 1 /^ BFULL IAADDLFFIIADFI\n/
FP 1 /^           60        \n/
FC = 47
//

ID align-matcherprot-end2rev
AP matcher
CL -stdout -send2 -3 -srev1 -srev2
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +40\/68 \(58\.8%\)/
FP /^# Score: +198\n/
FP 1 /^             60        70\n/
FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/
FP 1 /^       ::::::: \. :::::\.:\.\n/
FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/
FP 1 /^               60        \n/
FC = 47
//

ID align-matcherprot-begendallrev
AP matcher
CL -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 -srev1 -srev2
IN ../../data/aligna.prot
IN ../../data/alignb.prot
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/11 \(54\.5%\)/
FP /^# Score: +32\n/
FP 1 /^           10     \n/
FP 1 /^ AFULL AAEEFLFIIAA\n/
FP 1 /^ BFULL AADDFFILIAA\n/
FP 1 /^             10   \n/
FC = 44
//

ID align-wordmatch-same
AP wordmatch
CL tembl:v00294 tembl:v00294 -word 50 -auto
FI v00294.wordmatch
FC = 23
FP /^ +1113 +V00294 +[+] +1\.\.1113 +V00294 +[+] +1\.\.1113\n/
FI V00294.gff
FZ = 180
FP /^V00294\twordmatch\tsequence_feature\t1\t1113\t1\t/
FI wordmatch.log
FP /Number of patterns\/words found: 1064/
FP /Sum of match lengths: 1113/
//

ID align-wordmatch-pair
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat pair
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 1 /^HBA_HUMAN         59 HGKKV     63\n/
FP 1 /^                     \|\|\|\|\|\n/
FP 2 /^                     \|\|\|\|\n/
FP 1 /^HBB_HUMAN         64 HGKKV     68\n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /Number of all matches: 3/
//

ID align-wordmatch-srspair
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat srspair
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 1 /^HBA_HUMAN         59 HGKKV     63\n/
FP 1 /^                     \|\|\|\|\|\n/
FP 2 /^                     \|\|\|\|\n/
FP 1 /^HBB_HUMAN         64 HGKKV     68\n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /^EFTP/
FP /^HGKK/
//

ID align-wordmatch-markx0
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat markx0
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 1 /^HBA_HU HGKKV\n/
FP 1 /^       :::::\n/
FP 1 /^HBB_HU HGKKV\n/
FP 1 /^       60   \n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /^WGKV/
//

ID align-wordmatch-markx1
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat markx1
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 1 /^HBA_HU HGKKV\n/
## found for numbering and for alignment in first hit
FP 2 /^           \n/
FP 1 /^HBB_HU HGKKV\n/
FP 1 /^       60   \n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /^HGKK.*5.0/
//

ID align-wordmatch-markx2
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat markx2
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 1 /^       60   \n/
FP 1 /^HBA_HU HGKKV\n/
FP 1 /^HBB_HU -----\n/
FP 2 /^HBB_HU ----\n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /Average match length: 4.33/
//

ID align-wordmatch-markx3
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat markx3
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 1 /^>HBA_HUMAN \.\.\nHGKKV\n/
FP 1 /^>HBB_HUMAN \.\.\nHGKKV\n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /^EFTP.*4.0/
//

ID align-wordmatch-markx10
AP wordmatch
CL tsw:hba_human tsw:hbb_human -aformat markx10
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI hba_human.wordmatch
FZ > 608
FP 3 /^>HBA_HUMAN \.\.\n/
FP 3 /^; sq_len: 142\n/
FP 1 /^; al_start: 59\n/
FP 1 /^; al_stop: 63\n/
FP 1 /^; al_display_start: 59\n/
FP 2 /^HGKKV\n/
FP 3 /^>HBB_HUMAN \.\.\n/
FP 3 /^; sq_len: 147\n/
FP 1 /^; al_start: 64\n/
FP 1 /^; al_stop: 68\n/
FP 1 /^; al_display_start: 64\n/
FI HBA_HUMAN.gff
FZ = 360
FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\t/
FI HBB_HUMAN.gff
FZ = 360
FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\t/
FI wordmatch.log
FP /^HGKK.*5.0/
//

ID align-merger-fasta
AP merger
CL -aformat fasta
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 108
FP /accggaaaaaaga\n[-]+\n/
FP /^---------------------gtgaatgaagtcgcttaagcaatcaatgtcggatgcggc\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//
ID align-merger-markx0
AP merger
CL -aformat markx0
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 421
FP /^# Score: 795\.0\n/
FP / 1340      1350\nV00295 cgctt/
FP /^V00295 cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/
FP /^X51872 [-]+gtgaatgaa\n +\n/
FP /^X51872 .*tccgaccaac\n      10/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-markx1
AP merger
CL -aformat markx1
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 421
FP /^# Score: 795\.0\n/
FP / 1340      1350\nV00295 cgctt/
FP /^V00295 cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/
FP /^X51872 [-]+gtgaatgaa\n +\n/
FP /^X51872 .*tccgaccaac\n      10/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//


ID align-merger-markx2
AP merger
CL -aformat markx2
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 293
FP /^# Score: 795\.0\n/
FP / 1340      1350\nV00295 cgctt/
FP /^V00295 cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/
FP /^V00295 [acgt]+gtgaatgaa\nX51872 [-]+\.\.\.\.\.\.\.\.\.\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-markx3
AP merger
CL -aformat markx3
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 167
FP /^# Score: 795\.0\n/
FP /^cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/
FP /^-----------------------------------------gtgaatgaa\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-markx10
AP merger
CL -aformat markx10
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 188
FP /^; sw_score: 795\.0\n/
FP /^cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/
FP /^-----------------------------------------gtgaatgaa\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-match
AP merger
CL -aformat match
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 30
FP /^   159 V00295 +[+] +1342\.\.1500     X51872 +[+] +1\.\.159\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-msf
AP merger
CL -af msf
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 265
FP /^V00295 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/
FP /^X51872 +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gtgaatgaa\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-pair
AP merger
CL -aformat pair
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FZ > 1445
FP /^# Score: 795\.0\n/
FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/
FP /^X51872 +1 [-]+gtgaatgaa +9\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-score
AP merger
CL -aformat score
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 9
FP 0 /^# Score:/
FP /^V00295 X51872 3173 \(795\.0\)\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-simple
AP merger
CL -aformat simple
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 293
FP /^# Score: 795\.0\n/
FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/
FP /^X51872 +1 [-]+gtgaatgaa +9\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-srs
AP merger
CL -aformat srs
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 229
FP /^# Score: 795\.0\n/
FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/
FP /^X51872 +1 [-]+gtgaatgaa +9\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-srspair
AP merger
CL -aformat srspair
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 293
FP /^# Score: 795\.0\n/
FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/
FP /^X51872 +1 [-]+gtgaatgaa +9\n/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-merger-tcoffee
AP merger
CL -aformat tcoffee
IN tembl:v00295
IN tembl:x51872
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00295.merger
FC = 167
FP /^2\nV00295 1500 ttccagct/
FP /^! score=795\.0\n/
FP /^1342 1 0 1 0\n/
FP /^1500 159 0 1 0\n/
FP 0 /^1501/
FI v00295.fasta
FC = 54
FZ = 3291
FP 1 /^>/
FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/
FP /ggaaaaaaga\ncttcgtggg/
//

ID align-needle-full
AP needle
CL -gapopen 16 -gapext 4 -stdout
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/64 \(12\.5%\)/
FP /^# Score: +24\.0\n/
FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg     50\n/
FP 1 /^      +              \|\|\|\|\.\.\|\.\.\|\|\|                          \n/
FP 1 /^BFULL +1 ------------aaacgggccttt--------------------------     12\n/
FC = 42
//

ID align-needle-part
AP needle
CL -gapopen 16 -gapext 4 -stdout
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +46\/67 \(68\.7%\)/
FP /^# Score: +162\.0\n/
FP 1 /^AFULL             48 ttgggccaattggcatg     64\n/
FP 1 /^                     \|\| \.\.\|\|\.\.\|\|      \n/
FP 1 /^APART             47 tt-aaccggtt------     56\n/
FC = 42
//

ID align-needle-begin
AP needle
CL -gapopen 16 -gapext 4 -stdout -sbegin1 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/60 \(13\.3%\)/
FP /^# Score: +24\.0\n/
FP 1 /^AFULL +5 aaccggttaaacccgggtttaaaaccccggggttttcccaaatttgggcc     54\n/
FP 1 /^      +          \|\|\|\|\.\.\|\.\.\|\|\|                 +\n/
FP 1 /^BFULL +1 --------aaacgggccttt------------------------------     12\n/
FP 1 /^BFULL +12 ----------     12\n/
FC = 43
//

ID align-needle-end
AP needle
CL -gapopen 16 -gapext 4 -stdout -send1 15
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +3\/24 \(12\.5%\)/
FP /^# Score: +15\.0\n/
FP 1 /^AFULL +1 acgtaaccggttaaa---------     15\n/
FP 1 /^BFULL +1 ------------aaacgggccttt     12\n/
FC = 39
//

ID align-needle-begin2
AP needle
CL -gapopen 16 -gapext 4 -stdout -sbegin2 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/64 \( 9\.4%\)/
FP /^# Score: +22\.0\n/
FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg     50\n/
FP 1 /^BFULL +5 --------------------------------gggccttt----------     12\n/
FC = 43
//

ID align-needle-end2
AP needle
CL -gapopen 16 -gapext 4 -stdout -send2 -3
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/64 \( 9\.4%\)/
FP /^# Score: +14\.0\n/
FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg     50\n/
FP 1 /^BFULL +1 ------------aaacgggcct----------------------------     10\n/
FC = 43
//

ID align-needle-begendall
AP needle
CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/11 \(45\.5%\)/
FP /^# Score: +21\.0\n/
FP 1 /^AFULL +5 aaccggttaaa     15\n/
FP 1 /^BFULL +2 aacggg-----      7\n/
FC = 42
//

ID align-needle-fullrev
AP needle
CL -gapopen 16 -gapext 4 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/64 \(12\.5%\)/
FP /^# Score: +24\.0\n/
FP /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt     15\n/
FP /^       +                                          \|\|\|\.\.\|\.\.\|\|\n/
FP /^BFULL +12 ----------------------------------------aaaggcccgt      3\n/
FC = 44
//

ID align-needle-partrev
AP needle
CL -gapopen 16 -gapext 4 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +4[4,6]\/6[6,7] \(6[6,8]\.7%\)/
FP /^# Score: +162\.0\n/
FP /^AFULL +1[6,7] g+tttaaccggttacgt      1\n/
FP /^      +   [\|]{10,13}    \n/
FP /^APART +1[2,3] g+tttaaccggtt----      1\n/
FC = 44
//

ID align-needle-beginrev
AP needle
CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/60 \(13\.3%\)/
FP /^# Score: +24\.0\n/
FP 1 /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt     15\n/
FP 1 /^      +                                           \|\|\|\.\.\|\.\.\|\|\n/
FP 1 /^BFULL +12 ----------------------------------------aaaggcccgt      3\n/
FC = 45
//

ID align-needle-endrev
AP needle
CL -gapopen 16 -gapext 4 -stdout -send1 15 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +3\/24 \(12\.5%\)/
FP /^# Score: +15\.0\n/
FP 1 /^AFULL +15 ---------tttaaccggttacgt      1\n/
FP 1 /^BFULL +12 aaaggcccgttt------------      1\n/
FC = 41
//

ID align-needle-begin2rev
AP needle
CL -gapopen 16 -gapext 4 -stdout -sbegin2 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/64 \( 9\.4%\)/
FP /^# Score: +22\.0\n/
FP /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt     15\n/
FP /^BFULL +12 -------aaaggccc-----------------------------------      5\n/
FC = 45
//

ID align-needle-end2rev
AP needle
CL -gapopen 16 -gapext 4 -stdout -send2 -3 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/64 \( 9\.4%\)/
FP /^# Score: +14\.0\n/
FP /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt     15\n/
FP /^BFULL +10 -aggcccgttt---------------------------------------      1\n/
FC = 45
//

ID align-needle-begendallrev
AP needle
CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -send1 15
CL -sbegin2 2 -send2 -6 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/11 \(45\.5%\)/
FP /^# Score: +21\.0\n/
FP /^AFULL +15 tttaaccggtt      5\n/
FP /^BFULL  +7 -----cccgtt      2\n/
FC = 44
//

ID needle-noendweight
AP needle
CL -gapopen=8 -gapextend=8 -stdout -datafile=EBLOSUM50 -endweight=no
IN asis::PAWHEAE
IN asis::HEAGAWGHEE
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +4\/11 \(36\.4%\)/
FP /^# Score: +25\.0\n/
FP /^asis               1 ---PAW-HEAE      7\n/
FP /^asis               1 HEAGAWGHEE-     10\n/
FC = 40
//

ID needle-endweight1
AP needle
CL -gapopen=8 -gapextend=8 -endopen=8 -endextend=8 -stdout
CL -datafile=EBLOSUM50 -endweight
IN asis::PAWHEAE
IN asis::HEAGAWGHEE
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/11 \(45\.5%\)/
FP /^# Score: +1\.0\n/
FP /^asis               1 -(-P)|(P-)|(PA)-(A)|(-)W-HEAE      7\n/
FP /^asis               1 HEAGAWGHE-E     10\n/
FC = 42
//

ID needle-endweight2
AP needle
CL asis:actggatatataatat asis:actaatat stdout -auto -endweight
CL -gapopen 20
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/16/
FP /^# Score: +16\.5/
FP /^asis +1 ac--------taatat/
FC = 39
//

ID needle-endweight3
AP needle
CL asis:actggatatataatat asis:actaatat stdout -auto -endweight
CL -gapopen 20 -gapextend 2 -endextend 1
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/16/
FP /^# Score: +6\.0/
FP /^asis +1 ac--------taatat/
FC = 41
//

ID needle-endweight4
AP needle
CL asis:actggatatataatat asis:actaatat stdout -auto -endweight
CL -gapopen 20 -gapextend 2 -endextend 0
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +6\/16/
FP /^# Score: +12\.0/
FP /^asis +1 --------actaatat/
FC = 41
//

ID needle-endweight5
AP needle
CL asis:MVL asis:MVHLLL stdout -aformat simple -endweight -auto
CL -gapopen 12 -gapextend 2
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +3\/6/
FP /^# Score: +-3\.0/
FP /^asis +1 MV---L /
FC = 41
//

ID needle-endweight6
AP needle
CL asis:MGQMQIV  asis:IVPPLKP stdout -aformat simple -endweight -auto
CL -endopen 0 -endextend 0
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +2\/12/
FP /^# Score: +8\.0/
FP /^asis +1 -----IVPPLKP /
FC = 41
//

ID needle-endweight7
AP needle
CL asis:IVPPLKP  asis:MGQMQIV stdout -aformat simple -endweight -auto
CL -endopen 0 -endextend 0
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +2\/12/
FP /^# Score: +8\.0/
FP /^asis +1 MGQMQIV----- /
FC = 41
//

ID needle-traceback1
AP needle
CL -auto -stdout -aformat simple -gapextend 1.0
CL asis::acgtaggtacgttttacgtacgtacgtacgtaaacaggtg
CL asis::acgtagaacgtacgtacgtacgtacacgcataagcggcag
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +28\/48 \(58\.3%\)/
FP /^# Score: +94\.0\n/
FP /^asis +1 acgtaggtacgttttacgtacgtacgtacgtaaac----aggtg----     40\n/
FP /^asis +1 acgtag--------aacgtacgtacgtacgtacacgcataagcggcag     40\n/
FC = 39
//

ID needle-traceback2
AP needle
CL -auto -stdout -aformat simple -gapextend 0.5
CL asis::tgcgcaggatgtccttccaa
CL asis::caatagactggtccgttcgc
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +12\/28 \(42\.9%\)/
FP /^# Score: +17\.0\n/
FP /^asis +1 tgcgcaggat------gtcc-ttc-caa/
FP /^asis +1 ----ca--atagactggtccgttcgc--/
FC = 39
//

ID needle-traceback3
AP needle
CL -auto -stdout
CL asis::CDISRILQTHADAKVQVLDNQNVSNGCVSKILGRYYETG
CL asis::CDISRILQ--------------VSNGCVSKILGRYYETG
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +25\/39 \(64\.1%\)/
FP /^# Score: +115\.5\n/
FP /^asis +1 CDISRILQTHADAKVQVLDNQNVSNGCVSKILGRYYETG/
FP /^asis +1 CDISRILQ--------------VSNGCVSKILGRYYETG/
FC = 37
//

ID needle-indel
AP needle
CL asis:cttttcgtggtatta asis:gcgaccatgagagag
CL -auto -gapo 1 -gape 1 -endw -endo 1 -ende 1 stdout
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/23 \(30\.4%\)/
FP /^# Gaps:    +16\/23 \(69\.6%\)/
FP /^# Score: +19\.0\n/
FP /^asis +1 (ctttt-)|(-ctttt)cg----tg-gta[ta-]{5}/
FP                         / +||    || | |   |/
FP /^asis +1 (-----g)|(g-----)cgaccatgag-a[ga-]{5}/
FC = 42
//

ID needle-simple1
AP needle
CL asis:aag asis:gg stdout -auto -endw
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +1\/3 \(33\.3%\)/
FP /^# Gaps:    +1\/3 \(33\.3%\)/
FP /^# Score: +-9\.0\n/
FP /^asis +1 aag/
FP / +       \.|/
FP /^asis +1 -gg/
FC = 38
//

ID needle-simple2
AP needle
CL asis:aa asis:gg stdout -auto
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity:   +0\/4 \( 0\.0%\)/
FP /^# Similarity: +0\/4 \( 0\.0%\)/
FP /^# Score: 0\.0\n/
FP /^asis +1 aa--/
FP /^asis +1 --gg/
FC = 37
//

ID needleall-withendweight
AP needleall
CL -auto -stdout -endweight -aformat simple
CL asis::DVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFV\
CL FYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEV
CL asis::RDDEERPMILIAGGTGFSYARSILLTALARNPNRDITIYWGGREEQHLYDLCELEALSLKHPGLQVV\
CL PVVEQPEAGWRGRTGTVLTAVLQDHGTLAEHDIYIAGRFEMAKIARDLFCSERNAREDRLFGDA
FI needleall.error
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +32\/155 \(20\.6%\)/
FP /^# Score: +62\.5\n/
FP /^asis +43 ----REEQHLYDLCEL------------EALSLKHPGLQVVPVVEQPEAG/
FP /^asis +96 ------SIL---------LPDADYYICGPIPFMRMQHDAL-KNLGIHEAR/
FC = 51
//

ID needleall-noendweight
AP needleall
CL -auto -stdout -noendweight
CL asis::DVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFV\
CL FYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEV
CL asis::RDDEERPMILIAGGTGFSYARSILLTALARNPNRDITIYWGGREEQHLYDLCELEALSLKHPGLQVV\
CL PVVEQPEAGWRGRTGTVLTAVLQDHGTLAEHDIYIAGRFEMAKIARDLFCSERNAREDRLFGDA
FI needleall.error
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^asis asis 156 \(63.5\)\n/
FC = 4
//

ID align-wordfinder-sam
AP wordfinder
CL -lowmatch 7 -stdout -auto -aformat sam -sformat2 fastq-sanger
CL ../../data/illumina_adapter_primer.fa
CL ../../data/test1_illumina.fastq
FI stderr
FI wordfinder.error
FP /Target 7 FC12044_91407_8_200_10_437 matches 4/
FC = 70
FI stdout
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FC = 23
FP /_8_200_303_427.*_DpnII_Gex_Adapters1_2\t8.*6H11M.*XXXIXFQXXXO.*NM:i:2/
//

ID align-wordmatch-sam
AP wordmatch
CL -wordsize 7 -stdout -auto -aformat sam -sformat2 fastq-sanger
CL ../../data/illumina_adapter_primer.fa -nodumpfeat 
CL ../../data/test1_illumina.fastq
FI stderr
FI wordmatch.log
FP /Average match length: 7.38/
FC = 32
FI stdout
FP /^FC12044_91407_8_200_10_437.*CTGCTTG	SXSXXXX	AS:i:7	NM:i:0/
FI Illumina_Genomici_DNA_Adapters1_1.gff
FC = 0
FI FC12044_91407_8_200_406_24.gff
FC = 0
//

ID align-supermatcher-sam
AP supermatcher
CL -word 7 -stdout -auto -aformat sam -sformat1 fastq-sanger
CL ../../data/test1_illumina.fastq
CL ../../data/illumina_adapter_primer.fa 
FI stderr
FI supermatcher.error
FP /No.*start points for.*_8_200_285_136 vs .*_Small_RNA_sequencing_primer/
FC = 754
FI stdout
FP /_427.*DpnII_Gex_A.*1_2.*6H7M3I9M.*CAGAGTTTTGCTCTTGTCC.*XXXIXFQXXXOIQSSXUFF/
FP /_437.*Small_RNA_3p_Adapter\t15.*1H7M.*CTGCTTG	SXSXXXX	AS:i:35.0	NM:i:0/
//

ID align-water-sam1
UC example from SAM paper(Bioinformatics 2009 August)
AP water
CL -auto -aformat sam -dataf EDNASIMPLE -outf stdout -gapo 2
CL asis:AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
CL asis:TTAGATAAAGGATACTG
FI stdout
FP /.*\t7\t.*\t8M2I4M1D3M\t.*\tTTAGATAAAGGATACTG\t.*\tAS:i:10.5\tNM:i:0/
//

ID align-water-sam2
AP water
CL -auto -aformat sam -datafile EDNASIMPLE -outfile stdout
CL asis:AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
CL asis:gcctaAGCTAA
FI stdout
FP /.*\t9\t.*\t5H6M\t.*\tAGCTAA\t.*\tAS:i:4.0\tNM:i:1/
//

ID align-water-sam3
AP water
CL -auto -srev2 -aformat sam -datafile EDNASIMPLE -outfile stdout
CL asis:AGCATGTTAGATAANNGANAGCTGTGCTAGTAGGCAGTCAGCGCCAT
CL asis:gcctaAGCTAA
FI stdout
FP /.*\t31\t.*\t6H5M\t.*\ttaggc\t.*\tAS:i:5.0\tNM:i:0/
//

ID align-water-full
AP water
CL -gapopen 5 -gapext 1 -stdout
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\.0\n/
FP 1 /^AFULL             13 aaacccggg--ttt     24\n/
FP 1 /^BFULL              1 aaa--cgggccttt     12\n/
FC = 38
//

ID align-water-part
AP water
CL -gapopen 5 -gapext 1 -stdout
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +46\/62 \(74\.2%\)/
FP /^# Score: +196\.0\n/
FP 1 /^AFULL +5 aaccggttaaacccgggtttaaaaccccggggtttt---cccaaatttgg     51\n/
FP 1 /^APART +1 aaccggttaaacccgggtttaaaaccccggggttttaaaccc------gg     44\n/
FC = 42
//

ID align-water-begin
AP water
CL -gapopen 5 -gapext 1 -stdout -sbegin1 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\.0\n/
FP 1 /^AFULL             13 aaacccggg--ttt     24\n/
FP 1 /^BFULL              1 aaa--cgggccttt     12\n/
FC = 39
//

ID align-water-end
AP water
CL -gapopen 5 -gapext 1 -stdout -send1 15
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/10 \(70\.0%\)/
FP /^# Score: +25\.0\n/
FP 1 /^AFULL              5 aaccgg--tt     12\n/
FP 1 /^BFULL              2 aacgggcctt     11\n/
FC = 39
//

ID align-water-begin2
AP water
CL -gapopen 5 -gapext 1 -stdout -sbegin2 5
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/9 \(77\.8%\)/
FP /^# Score: +29\.0\n/
FP 1 /^AFULL             50 gggccaatt     58\n/
FP 1 /^BFULL              5 gggcc--tt     11\n/
FC = 39
//

ID align-water-end2
AP water
CL -gapopen 5 -gapext 1 -stdout -send2 -3
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/11 \(72\.7%\)/
FP /^# Score: +30\.0\n/
FP 1 /^AFULL             44 aaatttgggcc     54\n/
FP 1 /^BFULL              1 aaa--cgggcc      9\n/
FC = 39
//

ID align-water-begendall
AP water
CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\.0\n/
FP 1 /^AFULL              5 aaccgg     10\n/
FP 1 /^BFULL              2 aacggg      7\n/
FC = 42
//

ID align-water-fullrev
AP water
CL -gapopen 5 -gapext 1 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\.0\n/
FP /^AFULL             24 aaa--cccgggttt     13\n/
FP /^BFULL             12 aaaggccc--gttt      1\n/
FC = 40
//


ID align-water-partrev
AP water
CL -gapopen 5 -gapext 1 -stdout -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignapart.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +46\/62 \(74\.2%\)/
FP /^# Score: +196\.0\n/
FP /^AFULL +58 aattgg-----cccaaatttggg---aaaaccccggggttttaaacccgg     17\n/
FP /^APART +56 aaccggttaaaccc------gggtttaaaaccccggggttttaaacccgg     13\n/
FC = 44
//

ID align-water-beginrev
AP water
CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +10\/14 \(71\.4%\)/
FP /^# Score: +38\.0\n/
FP 1 /^AFULL             24 aaa--cccgggttt     13\n/
FP 1 /^BFULL             12 aaaggccc--gttt      1\n/
FC = 41
//

ID align-water-endrev
AP water
CL -gapopen 5 -gapext 1 -stdout -send1 15 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/10 \(70\.0%\)/
FP /^# Score: +25\.0\n/
FP /^AFULL             12 aa--ccggtt      5\n/
FP /^BFULL             11 aaggcccgtt      2\n/
FC = 41
//

ID align-water-begin2rev
AP water
CL -gapopen 5 -gapext 1 -stdout -sbegin2 5 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +7\/9 \(77\.8%\)/
FP /^# Score: +29\.0\n/
FP /^AFULL             58 aattggccc     50\n/
FP /^BFULL             11 aa--ggccc      5\n/
FC = 41
//

ID align-water-end2rev
AP water
CL -gapopen 5 -gapext 1 -stdout -send2 -3 -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +8\/11 \(72\.7%\)/
FP /^# Score: +30\.0\n/
FP /^AFULL             54 ggcccaaattt     44\n/
FP /^BFULL              9 ggccc--gttt      1\n/
FC = 41
//

ID align-water-begendallrev
AP water
CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6
CL -srev1 -srev2
IN ../../data/aligna.dna
IN ../../data/alignb.dna
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FP /^# Identity: +5\/6 \(83\.3%\)/
FP /^# Score: +21\.0\n/
FP /^AFULL             10 ccggtt      5\n/
FP /^BFULL              7 cccgtt      2\n/
FC = 44
//

ID align-wordfinder-simple
AP wordfinder
CL -gapopen 10 -gapextend 1 -wordlen 3 -aformat simple -outfile align.simple
CL asis:GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGG asis:TCGTTT -auto
FI wordfinder.error
FC = 1
FP /matches 1/
FI align.simple
FC = 43
FP /^# Score: 21\.0/
FP /TCGTAT/
//

ID align-supermatcher-default
TI 400
AP supermatcher
CL @../../data/eclac.list tembl:j01636 -word 50 
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI supermatcher.error
FZ = 0
FI j01636.supermatcher
FZ > 71230
FP /^J01636 +1 /
FP /^# Score: 37385\.0/
FP 5 /^# Score: /
FP /^X51872 +1801 [acgt]+ +1832\n/
//

ID align-supermatcher-range
TI 400
AP supermatcher
CL @../../data/eclac.list tembl:j01636 -word 50 -sbegin2 101 -send2 -101
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI supermatcher.error
FZ = 0
FI j01636.supermatcher
FZ > 69555
FP /^J01636 +101 /
FP /^# Score: 36385\.0/
FP 5 /^# Score: /
FP /^X51872 +1701 [acgt]+ +1732\n/
//

ID align-supermatcher-defaultrev
TI 400
AP supermatcher
CL @../../data/eclac.list tembl:j01636 -word 50  -srev1 -srev2
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI supermatcher.error
FZ = 0
FI j01636.supermatcher
FZ > 71230
FP /^# Score: 37385\.0/
FP 5 /^# Score: /
FP /^X51872 +1832 [acgt]+ +1783\n/
FP /^X51872   +32 [acgt]+ +1\n/
//

ID align-supermatcher-rangerev
TI 400
AP supermatcher
CL @../../data/eclac.list tembl:j01636 -word 50 -sbegin2 101 -send2 -101 -srev1 -srev2
IN
IN 3.0
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout 
FZ = 0
FI supermatcher.error
FZ = 0
FI j01636.supermatcher
FZ > 69555
FP 3 /^J01636 +7277 /
FP /^# Score: 36385\.0/
FP 5 /^# Score: /
FP /^X51872 +32 [acgt]+ +1\n/
FP 2 /^J01636 +127 [acgt]+ +101\n/
//

ID supermatcher-simple
AP supermatcher
CL -gapopen 10 -gapextend 1 -wordlen 3 -aformat simple -outfile align.simple
CL asis:GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGG asis:TCGTTT -auto
FI supermatcher.error
FZ = 0
FI align.simple
FC = 41
FP /^# Score: 21\.0/
FP /TCGTAT/
//

ID supermatcher-minwidth
AP supermatcher
CL ../../data/aligna.dna ../../data/tropomyosin.fasta
CL -width 1 -gapopen 1 -gapextend 1 -aformat score -outfile align.score -auto
FI supermatcher.error
FP /.*BG089808.*/
FZ = 62
FI align.score
FZ = 372
FP /BF056441.* 12 \(33.0\)/
FP /BE848719.* 7 \(35.0\)/
FP /BF022813.* 6 \(30.0\)/
FP /BF452255.* 6 \(30.0\)/
FP /BG147728.* 6 \(30.0\)/
FP /BI817778.* 7 \(35.0\)/
FP /AF186109.* 6 \(30.0\)/
FP /AF186110.* 9 \(36.0\)/
FP /AF310722.* 9 \(36.0\)/
FP /AF362886.* 6 \(30.0\)/
FP /AF362887.* 6 \(30.0\)/
FP /AF087679.* 6 \(30.0\)/
//

ID supermatcher-minscore1
AP supermatcher
CL ../../data/aligna.dna ../../data/tropomyosin.fasta -auto
CL -minscore 120 -gapopen 1 -gapextend 1 -aformat score -outfile align.score
FI supermatcher.error
FP /.*BG089808.*/
FZ = 62
FI align.score
FZ = 343
FP /BF056441.* 84 \(132.0\)/
FP /BF022813.* 88 \(128.0\)/
FP /BF452255.* 88 \(128.0\)/
FP /BG147728.* 88 \(128.0\)/
FP /AF186109.* 82 \(146.0\)/
FP /AF186110.* 83 \(151.0\)/
FP /AF310722.* 83 \(151.0\)/
FP /AF362886.* 86 \(136.0\)/
FP /AF362887.* 85 \(125.0\)/
FP /AF087679.* 82 \(146.0\)/
//

ID supermatcher-minscore2
AP supermatcher
CL ../../data/aligna.dna ../../data/tropomyosin.fasta -minscore 35
CL -outfile align -auto  -gapextend 1 -width 12 -send2 172 -send1 50
FI supermatcher.error
FP /.*BG089808/
FP /.*BG147728/
FI align
FC = 88
FP /Score: 38.0/
FP /BF056441          30 tattccattgcacaatttg     48/
FP /                     |.||||    || ||||||/
FP /AFULL             37 ttttcc----ca-aatttg     50/
FP /Score: 40.0/
FP /BE848719         102 ggtgttaaaac    112/
FP /                     ||| |||||||/
FP /AFULL             20 ggt-ttaaaac     29/
FP /Score: 41.0/
FP /BI817778           1 ccgggg--taccctaa     14/
FP /                     ||||||  |.|||.||/
FP /AFULL             31 ccggggttttcccaaa     46/
//

ID supermatcher-wordlen7
AP supermatcher
CL ../../data/tropomyosin.fasta ../../data/aligna.dna
CL -gapextend 1 -wordlen 7 -outfile align -auto
FI supermatcher.error
FP /.*BG089808/
FP /.*BG147728/
FI align
FZ = 2850
FP /Score: 41.0/
FP /BE848719         102 ggtgttaaaacagtactcttctggttt-----agttt    133/
FP /                     ||| |||||||      |....|||||     |.|||/
FP /AFULL             20 ggt-ttaaaac------cccggggttttcccaaattt     49/
FP /Score: 42.0/
FP /AFULL             31 ccggggttttcccaaatttgggcc     54/
FP /                     ||||||  |.|||.||     |||/
FP /BI817778           1 ccgggg--taccctaa-----gcc     17/
FP /Score: 55.0/
FP /.*   3 gtaacc-------ggttaaacccg-ggtttaaaaccccggggttttccca     44/
FP /.*     ||.|||       |||    .||| ||   ||||.|      .|..|||./
FP /.* 740 gtgacctgaaggaggt----gccgcgg---aaaaac------atcaccct    776/
FP /AFULL             45 aatt-------tgggccaattggc     61/
FP /                     .|||       |||||||  ||||/
FP /AF310722         852 cattcggggtctgggcca--tggc    873/
//

ID wordfinder-simple
AP wordfinder
CL -gapopen 10 -gapextend 1 -wordlen 3 -aformat simple -outfile align.simple
CL asis:GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGG asis:TCGTTT -auto
FI wordfinder.error
FP /.*matches 1/
FZ = 24
FI align.simple
FC = 43
FP /^# Score: 21\.0/
FP /TCGTAT/
//

ID wordfinder-minwidth
AP wordfinder
CL ../../data/tropomyosin.fasta ../../data/aligna.dna
CL -width 1 -gapopen 1 -gapextend 1 -aformat score -outfile align.score -auto
FI wordfinder.error
FP /matches 12/
FC = 1
FI align.score
FZ = 373
FP /AFULL BF056441 17 \(31.0\)/
FP /.+BE848719 11 \(37.0\)/
FP /.+BF022813 6 \(30.0\)/
FP /.+BF452255 6 \(30.0\)/
FP /.+BG147728 6 \(30.0\)/
FP /.+BI817778 7 \(35.0\)/
FP /.+AF186109 6 \(30.0\)/
FP /.+AF186110 9 \(36.0\)/
FP /.+AF310722 9 \(36.0\)/
FP /.+AF362886 6 \(30.0\)/
FP /.+AF362887 6 \(30.0\)/
FP /.+AF087679 6 \(30.0\)/
//

ID wordfinder-minalignlen1
AP wordfinder
CL ../../data/tropomyosin.fasta ../../data/aligna.dna -auto
CL -lowalign 80 -gapopen 1 -gapextend 1 -aformat score -outfile align.score
FI wordfinder.error
FP /.*excludes 'BI817778'/
FC = 2
FI align.score
FC = 14
FP /.+BF056441 83 \(121.0\)/
FP /.+BE848719 88 \(146.0\)/
FP /.+BF022813 88 \(128.0\)/
FP /.+BF452255 88 \(128.0\)/
FP /.+BG147728 88 \(128.0\)/
FP /.+AF186109 86 \(142.0\)/
FP /.+AF186110 83 \(151.0\)/
FP /.+AF310722 83 \(151.0\)/
FP /.+AF362886 86 \(136.0\)/
FP /.+AF362887 87 \(147.0\)/
FP /.+AF087679 86 \(142.0\)/
//

ID wordfinder-minalignlen2
AP wordfinder
CL ../../data/tropomyosin.fasta ../../data/aligna.dna -lowalign 10
CL -outfile align -auto  -gapextend 1 -width 12 -send2 172 -send1 50
FI wordfinder.error
FP /.*matches 1/
FI align
FC = 44
FP /Score: 33.0/
FP /BF056441          37 ttgcacaatttg     48/
FP /                     ||.|..||||||/
FP /AFULL             39 ttcccaaatttg     50/
//

ID wordfinder-wordlen7
AP wordfinder
CL ../../data/aligna.dna ../../data/tropomyosin.fasta
CL -gapextend 1 -wordlen 7 -outfile align -auto
FI wordfinder.error
FP /.*BE848719 matches 1/
FC = 4
FI align
FC = 116
FP /Score: 35.0/
FP /AFULL             57 ttggcat     63/
FP /                     |||||||/
FP /BE848719          15 ttggcat     21/
//

#######################################
# EMBOSS make check
#######################################

ID ajtest-check
AQ ajtest
IN tembl:x13776
IN ../../data/globins.msf
IN stdout
IN abc.seq
IN abc.gff
FI stderr
FC = 2
FP 1 /Warning: /
FP 1 /Warning: No features written /
FP 0 /Error: /
FP 0 /Died: /
FI kim1.out
FZ = 4585
FP /^ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP\.\n/
FI abc.seq
FC = 0
FI abc.gff
FC = 0
//

ID ajtest-all-check
AQ ajtest
CL -nostdout -outfile ""
CL -outseq outseq
IN tembl:x13776
IN ../../data/globins.msf
IN abc.gff
FI stderr
FC = 2
FP 1 /Warning: /
FP 1 /Warning: No features written /
FP 0 /Error: /
FP 0 /Died: /
FI kim1.out
FZ = 4585
FP /^ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP\.\n/
FI outseq
FC = 0
FI abc.gff
FC = 0
FI x13776.nulloutfile
FC = 0
//

ID complex-check
AQ complex
TI 300
CL -omnia
IN tembl:x*
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI complex.ujtable
FZ = 0
FI x59796.complex
FZ = 1438
FP /^ +5 +X07523 +1658 +0\.7314 +\n/
FI x59796.fasta
FZ = 21112
FP 12 /^>/
//

ID corbatest-check
AQ corbatest
CC No documentation, no example
CL x13776 test.out
FI stderr
FC < 2
FP 1 /^CORBA support has not been compiled\n/
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID entrails-check
AQ entrails
CL -full
IN
FI outfile.entrails
FZ > 26000
FP /^ +taglist +string +"" +"Extra tags to report"\n/
FP /^ +ausashow +boolean +"N" +"Show the full USA in the alignment"\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID histogramtest-check
AQ histogramtest
CL -graph ps
IN
IN
IN
FI histogramtest.ps
FZ > 0
FP /^%%/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^Created histogramtest.ps\n/
//

# this test needs to be kept so stdin can be used for the
# valgrind test

ID intconv-check
AQ intconv
CL stdin stdout -auto
DL keep
IN int main (int argc, char* argv[]) {
IN   int number;
IN   long time;
IN   ajint long[52];
IN   ajlong int;
IN   exit (1);
IN }
FI stdout
FP 4 /ajint/
FP 2 /ajlong/
FZ = 107
//

ID patmattest-check
AQ patmattest
CC No documentation, no example
IN tembl:x13776
IN ACA
IN
FI stdout
FC = 93
FP /^ACA\n15 matches found\n/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID prima-check
AQ prima
CL -minplen 200 -maxplen 250
IN tembl:v00294
IN
IN
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI v00294.prima
FZ = 1259
FP /^2 pairs found\n/
FP / +266 TTGTCGCGGCGATTAAATCTC +286\s+510 GTACCGTCTTCATGGGAGAAA +530\n/
FP / +452 CTAATGTTCCGGCGTTATTT +471\s+696 TTTGTTGAAAACCGGACATG +715\n/
//

ID primers-check
RQ primer3
AQ primers
CC No documentation, no example
IN tembl:k00650
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI k00650.primers
FZ = 911
FP /\A\n# PRIMER3 RESULTS FOR K00650\n/
FP /^   1 PRODUCT SIZE: 264\n/
FP /^     FORWARD PRIMER    2492   20  60\.01  45\.00  AGAATCCGAAGGGAAAGGAA\n/
FP /^     REVERSE PRIMER    2755   20  59\.98  55\.00  CTTCTCCTTCAGCAGGTTGG\n/
//

ID seqinfo-check
AQ seqinfo
CC No documentation, no example
IN tembl:x13776
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 163
FP /^Length:[ \t]+2167 basepairs\n/
FP /^GC Content:[ \t]+66\.5436 %\n/
//

ID seqretall-check
AQ seqretall
IN @../../data/eclac.list
IN
FI j01636.fasta
FZ = 15619
FP 5 /^>/
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID seqretallfeat-check
AQ seqretallfeat
CL -osf embl
IN @../../data/eclac.list
IN x51872ll.embl
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI x51872ll.embl
FZ = 62309
FP 3 /^ID   V00/
FP 5 /^ID   /
//

ID seqretset-check
AQ seqretset
IN @../../data/eclac.list
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.fasta
FZ = 15619
FP 5 /^>/
//

ID seqretsingle-check
AQ seqretsingle
IN @../../data/eclac.list
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI j01636.fasta
FZ = 7679
FP 1 /^>/
//

ID testplot-check
AQ testplot
CC No documentation, no example
CL -graph ps
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^Created testplot\.ps\n/
FI testplot.ps
FC = 475
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID treetypedisplay-check
AQ treetypedisplay
CC No documentation, no example
CL -graph ps
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FC = 1
FP /^Created treetypedisplay\.ps\n/
FI treetypedisplay.ps
FC = 290
FP /^%%Title: PLplot Graph\n/
FP /^%%Pages: 1\n/
//

ID acd-calc-feat
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatestcalcfeat ../../data/feat.emft
IN
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 7 /:/
FP 1 /FLength \[32987\]: /
FP 1 /FName: /
FP 1 /FBegin \[1\]: /
FP 1 /FEnd \[32987\]: /
FP 1 /FProtein \[N\]:/
FP 1 /FNucleic \[Y\]: /
FP 1 /FSize \[62\]: /
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acd-calc-regexp
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatestcalcregexp "abc[def] ghi"
IN
FI stderr
FC = 2
FP 1 /:/
FP 1 /Length \[12\]: /
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acd-calc-seq
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatestcalcseq tembl:x13776
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 6 /:/
FP 1 /Length \[2167\]: /
FP 1 /Name \[X13776\]: /
FP 1 /Begin \[1\]: /
FP 1 /End \[2167\]: /
FP 1 /Protein \[N\]:/
FP 1 /Nucleic \[Y\]: /
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acd-calc-seqall
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatestcalcseqall @../../data/eclac.list
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 6 /:/
FP 1 /Length \[7477\]: /
FP 1 /Name \[J01636\]: /
FP 1 /Begin \[1\]: /
FP 1 /End \[7477\]: /
FP 1 /Protein \[N\]:/
FP 1 /Nucleic \[Y\]: /
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acd-calc-seqset
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatestcalcseqset @../../data/eclac.list
IN
IN
IN
IN
IN
IN
IN
IN
FI stderr
FC = 2
FP 8 /:/
FP 1 /Length \[7477\]: /
FP 1 /Name \[J01636\]: /
FP 1 /Begin \[1\]: /
FP 1 /End \[7477\]: /
FP 1 /Protein \[N\]:/
FP 1 /Nucleic \[Y\]: /
FP 1 /Totweight \[5\.000\]: /
FP 1 /Count \[5\]: /
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

ID acd-calc-string
AP acdc
PP EMBOSS_ACDROOT=../../acd
PP export EMBOSS_ACDROOT
CL qatestcalcstring "abc def"
IN
FI stderr
FC = 2
FP 1 /:/
FP 1 /Length \[7\]: /
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
//

####################################################
#
# multifield queries with query operators
#
####################################################

ID qsyn-idlist
AP seqret
CL "tsw-{id:hba_human | id:hbb_human}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 1 /^>HBB_HUMAN/
FP 2 /^>/
//

ID qsyn-idlist2
AP seqret
CL "tsw{hba_human, hbb_human}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 1 /^>HBB_HUMAN/
FP 2 /^>/
//

ID qsyn-idlist3
AP seqret
CL "tsw{hba_human|hbb_human}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 2 /^>/
//

ID qsyn-idlist4
AP seqret
CL "tsw-id{hba_human|hbb_human}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 2 /^>/
//

ID qsyn-idlist-mix1
AP seqret
CL "tsw{HBA_HUMAN, P68871}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 1 /^>HBB_HUMAN/
FP 2 /^>/
//

ID qsyn-idlist-mix2
AP seqret
CL "tsw{P68871, HBA_HUMAN}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 1 /^>HBB_HUMAN/
FP 2 /^>/
//

ID qsyn-idlist-mix3
AP seqret
CL "tsw{P68871, ABCDEF, HBA_HUMAN}" stdout -auto
FI stdout
FP 0 /^>HIRA_TAKRU/
FP 1 /^>HBA_HUMAN/
FP 1 /^>HBB_HUMAN/
FP 2 /^>/
//

ID qsyn-id-not
AP seqret
CL "tsw-{id:h* ! des:Hemoglobin}" stdout -auto
FI stdout
FP /^>HIRA_TAKRU/
FP 0 /^>HBA_HUMAN/
FP 2 /^>/
//

ID qsyn-id-not-nospace
AP seqret
CL "tsw-{id:h*!des:Hemoglobin}" stdout -auto
FI stdout
FP /^>HIRA_TAKRU/
FP 0 /^>HBA_HUMAN/
FP 2 /^>/
//

ID qsyn-id2-not
AP seqret
CL "qanxflatall-{id:m1190* ! des:1a}" stdout -auto
FI stdout
FP /^>M11905/
FP 0 /^>M11903/
FP 2 /^>/
//

ID qsyn-acc-not
AP seqret
CL "qanxflatall-{acc:x01958 ! des:1a}" stdout -auto
FI stdout
FP /^>M11905/
FP 0 /^>M11903/
FP 2 /^>/
//

ID qsyn-part1
AP ontoget
CL "edam-{des:cdna}" stdout -auto
FI stdout
FP 1 /def: .*mRNA.*EST.*cDNA/
FP 3 /^id: /
//

ID qsyn-part2
AP ontoget
CL "edam-{des:mrna}" stdout -auto
FI stdout
FP 1 /def: .*mRNA.*EST.*cDNA/
FP 9 /^id: /
//

ID qsyn-and
AP ontoget
CL "edam-{des:cdna & des:mrna}" stdout -auto
FI stdout
FP 1 /def: .*mRNA.*EST.*cDNA/
FP 1 /^id: /
//

ID qsyn-eor
AP ontoget
CL "edam-{des:cdna ^ des:mrna}" stdout -auto
FI stdout
FP 0 /def: .*cDNA or mRNA/
FP 2 /def: .*cDNA/
FP 8 /def: .*mRNA/
FP 10 /^id: /
//

ID qsyn-not
AP ontoget
CL "edam-{nam:rna ! des:sequence}" stdout -auto
FI stdout
FP 0 /def:.*sequence /
FP 6 /def:.*sequences/
FP 25 /^id: /
//

####################################################
#
# query syntax operators by access method
#
####################################################

ID qacc-or-emboss
AP seqret
CL "qanxflat-id{m11903 | m11904 | m11905}" stdout -auto
FI stdout
FP 3 /^>/
FP 3 /^>M1190/
//

ID qacc-and-emboss
AP seqret
CL "qanxflat-acc{x01958 & m11905}" stdout -auto
FI stdout
FP 1 /^>/
FP 1 /^>M11905/
//

ID qacc-eor-emboss
AP seqret
CL "qanxflat-acc{x01958 ^ m11905}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>M11905/
FP 1 /^>M11903/
FP 1 /^>M11904/
//

ID qacc-not-emboss
AP seqret
CL "qanxflat-acc{x01958 ! m11905}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>M11905/
FP 1 /^>M11903/
FP 1 /^>M11904/
//

ID qacc-or-emblcd
AP seqret
CL "qanflat-id{m11903 | m11904 | m11905}" stdout -auto
FI stdout
FP 3 /^>/
FP 3 /^>M1190/
//

ID qacc-and-emblcd
AP seqret
CL "qanflat-acc{x01958 & m11905}" stdout -auto
FI stdout
FP 1 /^>/
FP 1 /^>M11905/
//

ID qacc-eor-emblcd
AP seqret
CL "qanflat-acc{x01958 ^ m11905}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>M11905/
FP 1 /^>M11903/
FP 1 /^>M11904/
//

ID qacc-not-emblcd
AP seqret
CL "qanflat-acc{x01958 ! m11905}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>M11905/
FP 1 /^>M11903/
FP 1 /^>M11904/
//

ID qacc-or-embossgcg
AP seqret
CL "qanxgcg-id{v00294 | v00295 | v00296}" stdout -auto
FI stdout
FP 3 /^>/
FP 3 /^>V0029/
//

ID qacc-and-embossgcg
AP seqret
CL "qanxgcg-acc{v0029* & v00295}" stdout -auto
FI stdout
FP 1 /^>/
FP 1 /^>V00295/
//

ID qacc-eor-embossgcg
AP seqret
CL "qanxgcg-acc{v0029* ^ v00295}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>V00295/
FP 1 /^>V00294/
FP 1 /^>V00296/
//

ID qacc-not-embossgcg
AP seqret
CL "qanxgcg-acc{v0029* ! v00295}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>V00295/
FP 1 /^>V00294/
FP 1 /^>V00296/
//

ID qacc-or-gcg
AP seqret
CL "qangcg-id{v00294 | v00295 | v00296}" stdout -auto
FI stdout
FP 3 /^>/
FP 3 /^>V0029/
//

ID qacc-and-gcg
AP seqret
CL "qangcg-acc{v0029* & v00295}" stdout -auto
FI stdout
FP 1 /^>/
FP 1 /^>V00295/
//

ID qacc-eor-gcg
AP seqret
CL "qangcg-acc{v0029* ^ v00295}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>V00295/
FP 1 /^>V00294/
FP 1 /^>V00296/
//

ID qacc-not-gcg
AP seqret
CL "qangcg-acc{v0029* ! v00295}" stdout -auto
FI stdout
FP 2 /^>/
FP 0 /^>V00295/
FP 1 /^>V00294/
FP 1 /^>V00296/
//

ID qacc-or-srswww
AP seqret
CL "srs:uniprot-id{bgal_ecoli | lacy_ecoli | thga_ecoli}" stdout -auto
FI stdout
FP 3 /^>/
FP 3 /^>...._ECOLI /
//

ID qacc-and-srswww
AP seqret
CL "srs:uniprot-acc{p07464 & p77862}" stdout -auto
FI stdout
FP 1 /^>/
FP 1 /^>THGA_ECOLI /
//

ID qacc-eor-srswww-fail
ER 1
AP seqret
CL "srs:uniprot-acc{p07464 ^ p77862}" stdout -auto
FI stderr
FP 0 /Warning: /
FP 2 /Error: /
FP 1 /Died: /
FP /^Error: Query link operator '\^' not supported by access method 'srswww'/
//

ID qacc-not-srswww
AP seqret
CL "srs:uniprot-acc{p00274 ! p0aa28}" stdout -auto
FI stdout
FP 5 /^>/
FP 0 /^>THIO_SALTY/
FP 1 /^>THIO_SHIFL/
FP 1 /^>THIO_ECOLI/
//

####################################################
#
# chado access method for gmod.org chado schemas
#
####################################################

ID chado-genedb-chromosome
RQ postgresql
AP featcopy
CL tgenedb:NCLIV_chrIb -auto
FI ncliv_chrib.gff
FP 2285 /^NCLIV_chrIb/
## sequence-region range: 1 1908326
FP 1 /^##sequence-region NCLIV_chrIb/
//

ID chado-genedb-gene
RQ postgresql
AP featcopy
CL tgenedb:LinJ.18.0820 stdout -auto
FI stdout
FP 4 /^LinJ.18/
## sequence-region range: 329420	337405
FP 1 /^##sequence-region LinJ.18/
//

ID chado-flybase-transcript
RQ postgresql
AP featcopy
CL tflybase:FBtr0076663 -auto
FI 3l.gff
FP /^3L/
## sequence-region range: 8400369 8404675
FP 1 /^##sequence-region 3L/
FI stderr
FC < 5
//

ID chado-flybase-gene
RQ postgresql
AP featcopy
CL tflybase:FBgn0030105 FBgn0030105.gff -auto
FI FBgn0030105.gff
FP /^X/
## sequence-region range: 9110926 9111401
FP 1 /^##sequence-region X/
FP 1 /9110905.9110958.*five_prime_UTR_FBgn0030105.*FBtr0071309.*parent_type=mRNA/
FP 1 /CDS.*9110959.9111128.*ID=CDS_FBgn0030105.*Parent=FBtr0071309;/
FP 1 /intron.*9111129.9111181.*;Parent=FBtr0071309;Name=CG15369-in;/
//

###############################################################################
#
# test related to assembly formats, SAM/BAM and MIRA's MAF
#
###############################################################################

ID assemblyget-ex
AP assemblyget
CL bam::../../data/samspec1.4example.bam -oformat sam -auto
FI 4example.sam
FC = 9
FP 7 /ref/
FP 1 /r001	163	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG/
FP 1 /r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT/
//

ID assemblyget-bam2sam
AP assemblyget
CL bam::../../data/samspec1.4example.bam -oformat sam stdout -auto
FI stdout
FC = 9
FP 1 /@HD	VN:1.3	SO:coordinate/
FP 7 /ref/
FP 1 /r001	163	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG/
FP 1 /r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT/
//

ID assemblyget-bam2bam-keep
AP assemblyget
CL bam::../../data/samspec1.4example.bam
CL -oformat bam samspec1.4example.bam -auto -debug
DL keep
FI samspec1.4example.bam
FZ = 303
FP /.*/
FI samspec1.4example.bam.bai
FZ = 96
FP /^BAI\001/
FI assemblyget.dbg
FP /# bam targets = 1/
//

ID assemblyget-newbam2sam
AP assemblyget
CL bam::../assemblyget-bam2bam-keep/samspec1.4example.bam -oformat sam stdout -auto
FI stdout
FC = 9
FP 1 /@HD	VN:1.3	SO:coordinate/
FP 7 /ref/
FP 1 /r001	163	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG/
FP 1 /r003	0	ref	9	30	5H6M	\*	0	0	AGCTAA	\*	NM:i:1/
FP 1 /r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT/
//

ID seqret-bam2sam
AP seqret
CL bam::../../data/samspec1.4example.bam -osformat sam stdout -auto
FI stdout
FC = 8
FP 1 /r001.*TTAGATAAAGGATACTG/
FP 1 /r001.*CAGCGCCAT/
//

ID seqret-bam2bam
AP seqret
CL bam::../../data/index_test.bam -osformat bam check.bam -auto
FI check.bam
FZ = 440026
FP /^\001/
//

ID assemblyget-bamquery
AP assemblyget
CL bam::../../data/chr1to10.bam:chr1 -oformat sam stdout -auto -cbegin 1 -cend 1000
FI stdout
FC = 103
FP 100 /\tchr1\t/
FP 1 /Read_0\t0\tchr1\t1\t0\t100M\t\*\t0\t0/
//

ID assemblyget-bamquery-case
AP assemblyget
CL bam::../../data/chr1to10.bam:Chr1 -oformat sam stdout -auto -cbegin 1 -cend 1000
FI stdout
FC = 103
FP 100 /\tchr1\t/
FP 1 /Read_0\t0\tchr1\t1\t0\t100M\t\*\t0\t0/
//

ID assemblyget-bamquery2bam-keep
AP assemblyget
CL bam::../../data/chr1to10.bam:chr4 -oformat bam chr1to10.bam
CL -auto -cbegin 1 -cend 1000 -debug
DL keep
FI chr1to10.bam
FZ = 574
FP /.*/
FI chr1to10.bam.bai
FZ = 96
FP /^BAI\001/
FI assemblyget.dbg
FP /# bam targets = 10/
//

ID assemblyget-newbam-query2sam
AP assemblyget
CL bam::../assemblyget-bamquery2bam-keep/chr1to10.bam:chr4
CL -oformat sam stdout -auto -cbegin 1 -cend 1000
FI stdout
FC = 103
FP 102 /chr4/
FP 1 /Read_0\t0\tchr4\t1\t0\t100M\t\*\t0\t0/
//

# currently reads in all contigs are returned when a BAM index not available
# this test needs to be updated once this has changed????
ID assemblyget-bamquery2bam2-keep
AP assemblyget
CL bam::../../data/index_test.bam:chrY -oformat bam chrY.bam -auto
DL keep
TI 600
FI chrY.bam
FZ = 597748
FP /.*/
FI chrY.bam.bai
FZ = 1621416
FP /^BAI\001/
//

ID assemblyget-newbam-query2sam2
AP assemblyget
CL bam::../assemblyget-bamquery2bam2-keep/chrY.bam:chrY
CL -oformat sam stdout -auto -cbegin 1 -cend 57411600
FI stdout
FP 1 /^@RG	ID:0	CN:broad	DT:2008-07-12	LB:Solexa-5464	PI:335	PL:illumina	PU:0.*5	SM:NA07051/
FP 1 /^@SQ	SN:chrY	LN:57772954	UR:.*fasta	M5:62f69d0e82a12af74bad85e2e4a8bd91	SP:Homo sapiens/
FP /6340295	99	chrY\t57411391	255	51M\t=\t57411539	198	[ACTG]*	\?*.*610/
//

ID assemblyget-bam2bam2-keep
AP assemblyget
CL bam::../../data/index_test.bam -oformat bam index_test.bam -auto
DL keep
FI index_test.bam
FZ = 597748
FP /.*/
FI index_test.bam.bai
FZ = 1621416
FP /^BAI\001/
//

ID assemblyget-newbam-queryChrM2sam
AP assemblyget
CL bam::../assemblyget-bam2bam2-keep/index_test.bam:chrM
CL -oformat sam stdout -auto -cbegin 1 -cend 16800
FI stdout
FC = 27
FP /3968040	163	chrM	1519	255	51M	=	1687	218	[ACTG]{51}	\?{30}>>>>>>>>@@>>>>>\?>>>>>/
FP /3968040	83	chrM	1687	255	51M	=	1519	-218	[ACTG]{51}	[79;<?]*	NM:i:2	RG:Z:0/
//

ID assemblyget-sam2sam
AP assemblyget
CL sam::../../data/samspec1.4example.sam -oformat sam stdout -auto
FI stdout
FC = 9
FP 1 /@HD	VN:1.3	SO:coordinate/
FP 1 /@SQ	SN:ref	LN:45/
FP 7 /ref/
FP 1 /r001	163	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG/
FP 1 /r002	0	ref	9	30	3S6M1P1I4M	\*	0	0	AAAAGATAAGGATA	\*/
FP 1 /r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT/
//

ID assemblyget-maf2maf
AP assemblyget
CL maf::../../data/miradocex.maf -oformat maf stdout -auto
FI stdout
FC = 25
FP 1 /RD\tU13a/
//

ID assemblyget-maf2sam
AP assemblyget
CL maf::../../data/miradocex.maf -oformat sam stdout -auto
FI stdout
FC = 6
FP 1 /^U13a05e07.t1\t0\tcontigname_s1\t1\t0\t6S24M10S/
//

ID infoassembly-ex
AP infoassembly
CL sam::../../data/samspec1.4example.sam stdout -auto
FI stdout
FC > 2
FP /ref	45	0.00	6	0	0.00	0.00/
//

ID infoassembly-ex2-qual
AP infoassembly
CL sam::../../data/xxx.sam stdout -auto -qual qualsdist.txt
FI stdout
FC > 2
FP /chr20	62435964	25.36	2	2	1.97/
FI qualsdist.txt
FP /27	53/
//

ID infoassembly-ex3-refseq
AP infoassembly
CL sam::../../data/samspec1.4example.sam stdout -auto
CL -ref ../../data/samspec1.4example.ref.fasta
FI stdout
FC > 2
FP /ref	45	0.00	6	3	1.82	46.67/
//

ID infoassembly-ex4-refseqandgcbias-sam
AP infoassembly
CL sam::../../data/samspec1.4example.sam stdout -auto -windowsize 10
CL -ref ../../data/samspec1.4example.ref.fasta -gc gcbias.txt
FI stdout
FC > 2
FP /ref	45	0.00	6	3	1.82	46.67/
FI gcbias.txt
FC > 1
FP /20	5	1	8	1.1333/
FP /40	4	0	0	0/
FP /60	4	1	0	1.4166/
//

ID infoassembly-specex-refseqandgcbias-bam
AP infoassembly
CL bam::../../data/samspec1.4example.bam stdout -auto -windowsize 10
CL -ref ../../data/samspec1.4example.ref.fasta -gc gcbias.txt
FI stdout
FC > 2
FP /ref	45	0.00	6	3	1.82	46.67/
FI gcbias.txt
FC > 1
FP /20	5	1	8	1.1333/
FP /40	4	0	0	0/
FP /60	4	1	0	1.4166/
//

###############################################################################
#
# tests related to variation formats, VCF/BCF
#
###############################################################################

ID variationget-vcf2bcf
AP variationget
CL ../../data/valid-4.1.vcf -oformat bcf check.bcf
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI check.bcf
FZ > 1180
FP 0 /abcdefg/
//

ID variationget-bcf2vcf
AP variationget
CL bcf::../../data/valid-4.1.bcf -oformat vcf check.vcf
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI check.vcf
FC = 37
FP /19	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:/
FP 10 /20\t[0-9]*/
//


##############################################################################
#
# Server access
#
##############################################################################

ID server-entrez-seq
AP entret
CL entrez:nucleotide:x13776 test.out
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 147
FP 1 /^LOCUS   /
FP /^LOCUS +X13776 +2167 bp +DNA +linear +BCT 14-NOV-2006$/
//

ID server-entrez-seq-accn
AP entret
CL entrez:nucleotide-accn:x13776 test.out
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 147
FP 1 /^LOCUS   /
FP /^LOCUS +X13776 +2167 bp +DNA +linear +BCT 14-NOV-2006$/
//

ID server-srs-seq
AP entret
CL srs:uniprot:amir_pseae test.out
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 126
FP 1 /^ID   /
FP /^ID   AMIR_PSEAE              Reviewed;         196 AA\.$/
FP /^DT   01-MAY-2013, entry version 98\.$/
//

ID server-srs-seq-acc
AP entret
CL srs:uniprot-acc:p10932 test.out
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 126
FP 1 /^ID   /
FP /^ID   AMIR_PSEAE              Reviewed;         196 AA\.$/
FP /^DT   01-MAY-2013, entry version 98\.$/
//