/usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 | #!/usr/bin/env python
"""Provides application controller for CMfinder v0.2"""
import os
from cogent.app.util import CommandLineApplication, \
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters
from sys import exit
from os.path import isfile
__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"
if 'CMfinder' not in os.environ:
raise RuntimeError, \
'cmfinder cannot run if the CMfinder environment variable is not set.'
class CMfinder(CommandLineApplication):
"""The application controller for CMfinder 0.2 application
Options:
-b Do not use BLAST search to locate anchors
-v Verbose. Print running information, and save intermediate
results
-c <number> The maximum number of candidates in each sequence. Default
40. No bigger than 100.
-m <number> The minimum length of candidates. Default 30
-M <number> The maximum length of candidates. Default 100
-n <number> The maximum number of output motifs. Default 3
-f <number> The fraction of the sequences expected to contain the
motif. Default 0.80
-s <number> The number of stem-loops in the motif
-h Show help
"""
#-n default is 3, set to 3 because of resultpath concerns
_parameters = {
'-b':FlagParameter(Prefix='-',Name='b',Value=True),
'-v':FlagParameter(Prefix='-',Name='v'),
'-c':ValuedParameter(Prefix='-',Name='c',Value=None,Delimiter=' '),
'-m':ValuedParameter(Prefix='-',Name='m',Value=None,Delimiter=' '),
'-M':ValuedParameter(Prefix='-',Name='M',Value=None,Delimiter=' '),
'-n':ValuedParameter(Prefix='-',Name='n',Value=3,Delimiter=' '),
'-f':ValuedParameter(Prefix='-',Name='f',Value=None,Delimiter=' '),
'-s':ValuedParameter(Prefix='-',Name='s',Value=None,Delimiter=' ')}
_command = 'cmfinder.pl'
_input_handler = '_input_as_string'
def _get_result_paths(self,data):
"""Specifies the paths of output files generated by the application
data: the data the instance the application is called on
CMfinder produces it's output in two files .align and .motif
it also prints an output to sdtout.
"""
result={}
if not isinstance(data,list):
inputPath = str(data)
else:
inputPath=self._input_filename
itr=self.Parameters['-n'].Value
for i in range(itr):
nr=str(i+1)
try: #unknown nr of output files
f = open((inputPath+'.motif.h1.'+nr)) #if exists add to path
f.close()
result[('cm_'+nr)] =\
ResultPath(Path=(inputPath+'.cm.h1.'+nr))
result[('motif_'+nr)] =\
ResultPath(Path=(inputPath+'.motif.h1.'+nr))
except IOError: # else no more outputs
break
if self._input_filename is not None:
result['_input_filename'] = ResultPath(self._input_filename)
if isfile(self.WorkingDir+'latest.cm'):
result['latest'] =\
ResultPath(Path=(self.WorkingDir+'latest.cm'))
else:
pass
return result
class CombMotif(CommandLineApplication):
"""
Application controller for the combmotif.pl program
Only works for input as string since filnames are needed to located input
"""
_command = 'CombMotif.pl'
_input_handler = '_input_as_string'
def _input_as_string(self,data):
""" Return data as a string """
input = str(data) +' '+str(data)+'.motif'
return input
def _input_as_lines(self,data):
""" """
print 'Use input as string with cmfinder input_filename as input'
exit(1)
def _get_result_paths(self,data):
"""Specifies the paths of output files generated by the application
data: the data the instance of the application is called on
CombMotif will generate an output, the combination that was possible,
the modified _get_result_path will detect that output and return the
path to that output file. Since the output is not possible to predict
one has to try all possible outputs.
Assumes that one stem loop is used may correct this later
"""
result={}
filename = str(data)
motifList = []
mnr = 0 #motif number
if not isinstance(data,list):
inputPath = str(data)
else:
inputPath=self._input_filename
for h in range(2): #numbers of stem loops in each motif, recommended 1-2
if h == 0:
s = '.motif.h1.'
else:
s = '.motif.h2.'
for i in range(1,6):
for x in range(1,6): #two combined motifs
if x == i:
continue
try:
z = str(i)
w = str(x)
file = filename+s+z+'.'+w
f = open((file))
#print 'found',file
f.close()
mnr += 1
n = str(mnr)
result['comb'+n] = ResultPath(Path=file)
except IOError:
pass
for y in range(1,6): # three combined motifs
if y == x:
continue
try:
z = str(i)
w = str(x)
q = str(y)
file = filename+s+z+'.'+w+'.'+q
f = open((file))
#print 'found', file
f.close()
mnr += 1
n = str(mnr)
result['comb'+n] = ResultPath(Path=file)
except IOError:
pass
for k in range(1,6): # four combined motifs
if k == y:
continue
try:
z = str(i)
w = str(x)
q = str(y)
v = str(k)
file = filename+s+z+'.'+w+'.'+q+'.'+v
f = open(file)
#print 'found',file
f.close()
mnr += 1
n = str(mnr)
result['comb'+n] = ResultPath(Path=file)
except IOError:
pass
for j in range(1,6): #five combined motifs
if j == k:
continue
try:
z = str(i)
w = str(x)
q = str(y)
v = str(k)
u = str(j)
file = filename+s+z+'.'+w+'.'+q+'.'+v+'.'+u
f = open(file)
#print 'found',file
f.close()
mnr += 1
n = str(mnr)
result['comb'+n] = ResultPath(Path=file)
except IOError:
pass
if isfile(self.WorkingDir+'latest.cm'):
result['latest'] =\
ResultPath(Path=(self.WorkingDir+'latest.cm'))
else:
pass
return result
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