/usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py is in python-cogent 1.9-9.
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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 | #!/usr/bin/env python
#file: RNAshaper.py
"""
Author: Shandy Wikman (ens01svn@cs.umu.se)
Application controller for RNAshapes application
Revision History:
2006 Shandy Wikman created file
"""
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters, _find_synonym, is_not_None
__author__ = "Daniel McDonald and Greg Caporaso"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class RNAshapes(CommandLineApplication):
"""Application controller for RNAshapes application
Options:
-h Display this information
-H <option> Display detailed information on <option>
-v Show version
Sequence analysis modes:
-a Shape folding (standard mode)
-s Complete suboptimal folding
-p Shape probabilities
-q Shape probabilities (including shreps)
-P <value> Shape probabilities for mfe-best shapes
-i <value> Sampling with <value> iterations
-C Consensus shapes (RNAcast)
Additional modes (use with any of the above):
-r Calculate structure probabilities
-w <value> Specify window size
-W <value> Specify window position increment (use with -w) [1]
-m <shape> Match shape (use with -a, -s, -p, -q or -C)
Analysis control:
-e <value> Set energy range (kcal/mol)
-c <value> Set energy range (%) [10]
-t <value> Specify shape type (1-5) [5]
-F <value> Set probability cutoff filter (use with -p, -q or -P)
-T <value> Set probability output filter (use with -p, -q or -P)
-M <value> Set maximum loop length [30] (use -M n for unrestricted)
-l Allow lonely base pairs
-u Ignore unstable structures (use with -a, -s or -C)
Input/Output:
-o <value> Specify output type (1-4,f) [2]
-O <string> Specify output format string
-S <value> Specify output width for structures
-# <value> Print only the first <value> results
-g <value> Generate structure graphs for first <value> structures
-L Highlight upper case characters in structure graphs
-N Do not include additional information in graph output file
-f <file> Read input from <file>
-B Show progress bar (use with -p, -q or -P)
-z Enable colors (in interactive mode: disable colors)
-Z Enable colors for dotbracket and shape strings
-D <string> Convert dotbracket-string to shape (choose type with -t)
"""
_sequence_analysis = {
'-a':FlagParameter(Prefix='-',Name='a',Value=True),
'-s':FlagParameter(Prefix='-',Name='s',Value=False),
'-p':FlagParameter(Prefix='-',Name='p',Value=False),
'-q':FlagParameter(Prefix='-',Name='q',Value=False),
'-P':ValuedParameter(Prefix='-',Name='P',Value=None,Delimiter=' '),
'-i':ValuedParameter(Prefix='-',Name='i',Value=None,Delimiter=' '),
'-C':FlagParameter(Prefix='-',Name='C',Value=True)}
_additional_modes ={
'-r':FlagParameter(Prefix='-',Name='r',Value=False)}
_analysis_control = {
'-e':ValuedParameter(Prefix='-',Name='e',Value=None,Delimiter=' '),
'-c':ValuedParameter(Prefix='-',Name='c',Value=20,Delimiter=' '),
'-t':ValuedParameter(Prefix='-',Name='t',Value=None,Delimiter=' '),
'-F':ValuedParameter(Prefix='-',Name='F',Value=None,Delimiter=' '),
'-T':ValuedParameter(Prefix='-',Name='T',Value=None,Delimiter=' '),
'-M':ValuedParameter(Prefix='-',Name='M',Value=None,Delimiter=' '),
'-l':ValuedParameter(Prefix='-',Name='l',Value=None,Delimiter=' '),
'-u':ValuedParameter(Prefix='-',Name='u',Value=None,Delimiter=' ')}
_input_output = {
'-o':ValuedParameter(Prefix='-',Name='o',Value=None,Delimiter=' '),
'-S':ValuedParameter(Prefix='-',Name='S',Value=None,Delimiter=' '),
'-#':ValuedParameter(Prefix='-',Name='#',Value=None,Delimiter=' '),
'-g':ValuedParameter(Prefix='-',Name='g',Value=None,Delimiter=' '),
'-L':FlagParameter(Prefix='-',Name='L',Value=False),
'-N':FlagParameter(Prefix='-',Name='N',Value=False),
'-f':ValuedParameter(Prefix='-',Name='f',Delimiter=' '),
'-B':FlagParameter(Prefix='-',Name='B',Value=False),
'-z':FlagParameter(Prefix='-',Name='z',Value=False),
'-Z':FlagParameter(Prefix='-',Name='Z',Value=False)}
_parameters = {}
_parameters.update(_sequence_analysis)
_parameters.update(_additional_modes)
_parameters.update(_analysis_control)
_parameters.update(_input_output)
_command = 'RNAshapes'
_input_handler = '_input_as_string'
def _input_as_lines(self,data):
"""Makes data the value of a specific parameter"""
if data:
self.Parameters['-f']\
.on(super(RNAshapes,self)._input_as_lines(data))
return ''
def _input_as_string(self,data):
"""Makes data the value of a specific parameter
This method returns the empty string. The parameter will be printed
automatically once set.
"""
if data:
self.Parameters['-f'].on(data)
return ''
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