/usr/lib/python2.7/dist-packages/cogent/app/comrna.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 | #!/usr/bin/env python
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters, _find_synonym, is_not_None
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class comRNA(CommandLineApplication):
"""Application controller comRNA v1.80
for comRNA options type comRNA at the promt
"""
_parameters = {
'-L':ValuedParameter(Prefix='',Name='L',Value=None,Delimiter=' '),
'-E':ValuedParameter(Prefix='',Name='E',Value=None,Delimiter=' '),
'-S':ValuedParameter(Prefix='',Name='S',Value=None,Delimiter=' '),
'-Sh':ValuedParameter(Prefix='',Name='Sh',Value=None,Delimiter=' '),
'-Sl':ValuedParameter(Prefix='',Name='Sl',Value=None,Delimiter=' '),
'-P':ValuedParameter(Prefix='',Name='P',Value=None,Delimiter=' '),
'-n':ValuedParameter(Prefix='',Name='n',Value=None,Delimiter=' '),
'-x':ValuedParameter(Prefix='',Name='x',Value=None,Delimiter=' '),
'-m':ValuedParameter(Prefix='',Name='m',Value=None,Delimiter=' '),
'-tp':ValuedParameter(Prefix='',Name='tp',Value=None,Delimiter=' '),
'-ts':ValuedParameter(Prefix='',Name='ts',Value=None,Delimiter=' '),
'-a':ValuedParameter(Prefix='',Name='a',Value=None,Delimiter=' '),
'-o':ValuedParameter(Prefix='',Name='o',Value=None,Delimiter=' '),
'-c':ValuedParameter(Prefix='',Name='c',Value=None,Delimiter=' '),
'-j':ValuedParameter(Prefix='',Name='j',Value=None,Delimiter=' '),
'-r':ValuedParameter(Prefix='',Name='r',Value=None,Delimiter=' '),
'-f':ValuedParameter(Prefix='',Name='f',Value=None,Delimiter=' '),
'-v':ValuedParameter(Prefix='',Name='v',Value=None,Delimiter=' '),
'-g':ValuedParameter(Prefix='',Name='g',Value=None,Delimiter=' '),
'-d':ValuedParameter(Prefix='',Name='d',Value=None,Delimiter=' '),
'-wa':ValuedParameter(Prefix='',Name='wa',Value=None,Delimiter=' '),
'-wb':ValuedParameter(Prefix='',Name='wb',Value=None,Delimiter=' '),
'-wc':ValuedParameter(Prefix='',Name='wc',Value=None,Delimiter=' '),
'-wd':ValuedParameter(Prefix='',Name='wd',Value=None,Delimiter=' '),
'-we':ValuedParameter(Prefix='',Name='we',Value=None,Delimiter=' '),
'-pk':ValuedParameter(Prefix='',Name='pk',Value=None,Delimiter=' '),
'-pg':ValuedParameter(Prefix='',Name='pg',Value=None,Delimiter=' '),
'-pd':ValuedParameter(Prefix='',Name='pd',Value=None,Delimiter=' '),
'-ps':ValuedParameter(Prefix='',Name='ps',Value=None,Delimiter=' '),
'-pc':ValuedParameter(Prefix='',Name='pc',Value=None,Delimiter=' ')}
_command = 'comRNA'
_input_handler = '_input_as_string'
|