/usr/share/pyshared/cogent/app/pknotsrg.py is in python-cogent 1.5.1-2.
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 | #!/usr/bin/env python
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2011, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.1"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class PknotsRG(CommandLineApplication):
"""Application controller for PknotsRG v1.2 application
Input: plain seqeunce
pknotsRG is a tool for thermodynamic folding of RNA secondary
structures, including the class of canonical simple recursive
pseudoknots.
Options:
-m Use mfe strategy
-f Use enf strategy
-l Use loc strategy
-s Show suboptimals
-u no dangling bases (implies -s)
-o no suboptimals inside pknots (implies -s -l)
-e <value> Set energy range for suboptimals (kcal/mole)
-c <value> Set energy range for suboptimals (%) [10]
-n <value> Set npp-value [0.3]
-p <value> Set pkinit-value [9]
-k <value> Set maximal pknot-length
"""
_parameters = {
'-m':FlagParameter(Prefix='-',Name='m'),
'-f':FlagParameter(Prefix='-',Name='f'),
'-l':FlagParameter(Prefix='-',Name='l'),
'-s':FlagParameter(Prefix='-',Name='s'),
'-u':FlagParameter(Prefix='-',Name='u'),
'-o':FlagParameter(Prefix='-',Name='o'),
'-e':ValuedParameter(Prefix='-',Name='e',Delimiter=' '),
'-c':ValuedParameter(Prefix='-',Name='c',Delimiter=' '),
'-n':ValuedParameter(Prefix='-',Name='n',Delimiter=' '),
'-p':ValuedParameter(Prefix='-',Name='p',Delimiter=' '),
'-k':ValuedParameter(Prefix='-',Name='k',Delimiter=' ')}
_command = 'pknotsRG-1.2-i386-linux-static'
_input_handler = '_input_as_string'
def _input_as_string(self,filename):
"""Returns '>filename' to redirect input to stdin"""
return ''.join(['<',super(PknotsRG,self)._input_as_string(filename)])
def _input_as_lines(self,data):
"""Returns '>temp_filename to redirect input to stdin"""
return ''.join(['<',super(PknotsRG,self)._input_as_lines(data)])
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