/usr/lib/python2.7/dist-packages/cogent/app/dialign.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 | #!/usr/bin/env python
"""
Application controller for dialign2-2
"""
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.app.util import CommandLineApplication, ResultPath, \
get_tmp_filename, guess_input_handler
from random import choice
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
from cogent.parse.fasta import MinimalFastaParser
class Dialign(CommandLineApplication):
"""Dialign application controller"""
_options ={
# -afc Creates additional output file "*.afc" containing data of
# all fragments considered for alignment
# WARNING: this file can be HUGE !
'-afc':FlagParameter(Prefix='-',Name='afc'),
# -afc_v like "-afc" but verbose: fragments are explicitly printed
# WARNING: this file can be EVEN BIGGER !
'-afc_v':FlagParameter(Prefix='-',Name='afc_v'),
# -anc Anchored alignment. Requires a file <seq_file>.anc
# containing anchor points.
'-anc':FlagParameter(Prefix='-',Name='anc'),
# -cs if segments are translated, not only the `Watson strand'
# but also the `Crick strand' is looked at.
'-cs':FlagParameter(Prefix='-',Name='cs'),
# -cw additional output file in CLUSTAL W format.
'-cw':FlagParameter(Prefix='-',Name='cw'),
# -ds `dna alignment speed up' - non-translated nucleic acid
# fragments are taken into account only if they start with
# at least two matches. Speeds up DNA alignment at the expense
# of sensitivity.
'-ds':FlagParameter(Prefix='-',Name='ds'),
# -fa additional output file in FASTA format.
'-fa':FlagParameter(Prefix='-',Name='fa'),
# -ff Creates file *.frg containing information about all
# fragments that are part of the respective optimal pairwise
# alignmnets plus information about consistency in the multiple
# alignment
'-ff':FlagParameter(Prefix='-',Name='ff'),
# -fn <out_file> output files are named <out_file>.<extension> .
'-fn':ValuedParameter('-',Name='fn',Delimiter=' ', IsPath=True),
#
#
# -fop Creates file *.fop containing coordinates of all fragments
# that are part of the respective pairwise alignments.
'-fop':FlagParameter(Prefix='-',Name='fop'),
# -fsm Creates file *.fsm containing coordinates of all fragments
# that are part of the final alignment
'-fsm':FlagParameter(Prefix='-',Name='fsm'),
# -iw overlap weights switched off (by default, overlap weights are
# used if up to 35 sequences are aligned). This option
# speeds up the alignment but may lead to reduced alignment
# quality.
'-iw':FlagParameter(Prefix='-',Name='iw'),
# -lgs `long genomic sequences' - combines the following options:
# -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff,
# -fop, -ff, -cs, -ds, -pst
'-lgs':FlagParameter(Prefix='-',Name='lgs'),
# -lgs_t Like "-lgs" but with all segment pairs assessed at the
# peptide level (rather than 'mixed alignments' as with the
# "-lgs" option). Therefore faster than -lgs but not very
# sensitive for non-coding regions.
'-lgs_t':FlagParameter(Prefix='-',Name='lgs_t'),
# -lmax <x> maximum fragment length = x (default: x = 40 or x = 120
# for `translated' fragments). Shorter x speeds up the program
# but may affect alignment quality.
'-lmax':ValuedParameter('-',Name='lmax',Delimiter=' '),
# -lo (Long Output) Additional file *.log with information abut
# fragments selected for pairwise alignment and about
# consistency in multi-alignment proceedure
'-lo':FlagParameter(Prefix='-',Name='lo'),
# -ma `mixed alignments' consisting of P-fragments and N-fragments
# if nucleic acid sequences are aligned.
'-ma':FlagParameter(Prefix='-',Name='ma'),
# -mask residues not belonging to selected fragments are replaced
# by `*' characters in output alignment (rather than being
# printed in lower-case characters)
'-mask':FlagParameter(Prefix='-',Name='mask'),
# -mat Creates file *mat with substitution counts derived from the
# fragments that have been selected for alignment
'-mat':FlagParameter(Prefix='-',Name='mat'),
# -mat_thr <t> Like "-mat" but only fragments with weight score > t
# are considered
'-mat_thr':ValuedParameter('-',Name='mat_thr',Delimiter=' '),
# -max_link "maximum linkage" clustering used to construct sequence tree
# (instead of UPGMA).
'-max_link':FlagParameter(Prefix='-',Name='max_link'),
# -min_link "minimum linkage" clustering used.
'-min_link':FlagParameter(Prefix='-',Name='min_link'),
#
# -mot "motif" option.
'-mot':FlagParameter(Prefix='-',Name='mot'),
# -msf separate output file in MSF format.
'-msf':FlagParameter(Prefix='-',Name='msf'),
# -n input sequences are nucleic acid sequences. No translation
# of fragments.
'-n':FlagParameter(Prefix='-',Name='n'),
# -nt input sequences are nucleic acid sequences and `nucleic acid
# segments' are translated to `peptide segments'.
'-nt':FlagParameter(Prefix='-',Name='nt'),
# -nta `no textual alignment' - textual alignment suppressed. This
# option makes sense if other output files are of intrest --
# e.g. the fragment files created with -ff, -fop, -fsm or -lo
'-nta':FlagParameter(Prefix='-',Name='nta'),
# -o fast version, resulting alignments may be slightly different.
'-o':FlagParameter(Prefix='-',Name='o'),
#
# -ow overlap weights enforced (By default, overlap weights are
# used only if up to 35 sequences are aligned since calculating
# overlap weights is time consuming). Warning: overlap weights
# generally improve alignment quality but the running time
# increases in the order O(n^4) with the number of sequences.
# This is why, by default, overlap weights are used only for
# sequence sets with < 35 sequences.
'-ow':FlagParameter(Prefix='-',Name='ow'),
# -pst "print status". Creates and updates a file *.sta with
# information about the current status of the program run.
# This option is recommended if large data sets are aligned
# since it allows the user to estimate the remaining running
# time.
'-pst':FlagParameter(Prefix='-',Name='pst'),
# -smin <x> minimum similarity value for first residue pair (or codon
# pair) in fragments. Speeds up protein alignment or alignment
# of translated DNA fragments at the expense of sensitivity.
'-smin':ValuedParameter('-',Name='smin',Delimiter=' '),
# -stars <x> maximum number of `*' characters indicating degree of
# local similarity among sequences. By default, no stars
# are used but numbers between 0 and 9, instead.
'-stars':ValuedParameter('-',Name='stars',Delimiter=' '),
# -stdo Results written to standard output.
'-stdo':FlagParameter(Prefix='-',Name='stdo'),
# -ta standard textual alignment printed (overrides suppression
# of textual alignments in special options, e.g. -lgs)
'-ta':FlagParameter(Prefix='-',Name='ta'),
# -thr <x> Threshold T = x.
'-thr':ValuedParameter('-',Name='thr',Delimiter=' '),
# -xfr "exclude fragments" - list of fragments can be specified
# that are NOT considered for pairwise alignment
'-xfr':FlagParameter(Prefix='-',Name='xfr'),
}
_parameters = {}
_parameters.update(_options)
_command = "dialign2-2"
def _input_as_seqs(self,data):
lines = []
for i,s in enumerate(data):
#will number the sequences 1,2,3,etc.
lines.append(''.join(['>',str(i+1)]))
lines.append(s)
return self._input_as_lines(lines)
def _align_out_filename(self):
if self.Parameters['-fn'].isOn():
aln_filename = self._absolute(str(self.Parameters['-fn'].Value))
else:
raise ValueError, "No output file specified."
return aln_filename
def _get_result_paths(self,data):
result = {}
if self.Parameters['-fn'].isOn():
out_name = self._align_out_filename()
result['Align'] = ResultPath(Path=out_name,IsWritten=True)
return result
def getHelp(self):
"""Dialign help"""
help_str = """
"""
return help_str
|