/usr/share/pyshared/cogent/app/ilm.py is in python-cogent 1.5.3-2.
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 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 | #!/usr/bin/env python
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter,ValuedParameter,Parameters
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class ILM(CommandLineApplication):
"""Application controller ILM application
Predict a secondary structure given a score matrix
Main options:
-L l: minimum loop length (default=3)
-V v: minimum virtual loop length (default=3)
-H h: minimum helix length (default=3)
-N n: number of helices selected per iteration (default=1)
-I i: number of iterations before termination(default=unlimited)
"""
_parameters = {
'-L':ValuedParameter(Prefix='-',Name='L',Delimiter=' '),
'-V':ValuedParameter(Prefix='-',Name='V',Delimiter=' '),
'-H':ValuedParameter(Prefix='-',Name='H',Delimiter=' '),
'-N':ValuedParameter(Prefix='-',Name='N',Delimiter=' '),
'-I':ValuedParameter(Prefix='-',Name='I',Delimiter=' ')}
_command = 'ilm'
_input_handler = '_input_as_string'
class hlxplot(CommandLineApplication):
"""Application controller hlxplot application
Compute a helix plot score matrix from a sequence alignment
Options:
-b B: Set bad pair penalty to B
(Default = 2)
-g G: Set good pair score to G
(Default = 1)
-h H: Set minimum helix length to H
(Default = 2)
-l L: Set minimum loop length to L
(Default = 3)
-s S: Set helix length score to S
(Default = 2.0)
-t : Write output in text format
(Default = Binary format)
-x X: Set paired gap penalty to X
(Default = 3)
"""
_parameters = {
'-b':ValuedParameter(Prefix='-',Name='b',Delimiter=' '),
'-g':ValuedParameter(Prefix='-',Name='g',Delimiter=' '),
'-h':ValuedParameter(Prefix='-',Name='h',Delimiter=' '),
'-l':ValuedParameter(Prefix='-',Name='l',Delimiter=' '),
'-s':ValuedParameter(Prefix='-',Name='s',Delimiter=' '),
'-t':ValuedParameter(Prefix='-',Name='t',Delimiter=' '),
'-x':ValuedParameter(Prefix='-',Name='x',Delimiter=' ')}
_command = 'hlxplot'
_input_handler = '_input_as_string'
class xhlxplot(CommandLineApplication):
"""Application controller xhlxplot application
Compute an extended helix plot score matrix from a single sequence
Options:
-b B: Set bad pair penalty to B
(Default = 200)
-h H: Set minimum helix length to H
(Default = 2)
-l L: Set minimum loop length to L
(Default = 3)
-x X: Set paired gap penalty to X
(Default = 500)
-t : Write output in text format
(Default = Binary format)
-c : No Closing GU
(Default = allows closing GU)
"""
_parameters = {
'-b':ValuedParameter(Prefix='-',Name='b',Delimiter=' '),
'-h':ValuedParameter(Prefix='-',Name='h',Delimiter=' '),
'-l':ValuedParameter(Prefix='-',Name='l',Delimiter=' '),
'-x':ValuedParameter(Prefix='-',Name='x',Delimiter=' '),
'-t':ValuedParameter(Prefix='-',Name='t',Delimiter=' '),
'-c':ValuedParameter(Prefix='-',Name='c',Delimiter=' ')}
_command = 'xhlxplot'
_input_handler = '_input_as_string'
|