/usr/lib/python2.7/dist-packages/cogent/app/sfold.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 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | #!/usr/bin/env python
"""Application controller for Sfold application
Option -o sets output directory,default ../output/
If working directory is changed during the work flow option -o
need to be reset. -o is currently set to cwd
"""
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters
from os import getcwd
from sys import stderr
__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"
#IMPORTANT!!!!!
#must be specified if run outside sfold dir, default is ../param/
param_dir = 'your_path/sfold-2.0/param/'
class Sfold(CommandLineApplication):
"""Application controller Sfold application"""
cwd = getcwd()
_parameters = {
'-o':ValuedParameter(Prefix='-',Name='o',Delimiter=' ',Value=cwd),
'-a':ValuedParameter(Prefix='-',Name='a',Delimiter=' '),
'-f':ValuedParameter(Prefix='-',Name='f',Delimiter=' '),
'-l':ValuedParameter(Prefix='-',Name='l',Delimiter=' '),
'-m':ValuedParameter(Prefix='-',Name='m',Delimiter=' '),
'-w':ValuedParameter(Prefix='-',Name='w',Delimiter=' '),
'-p':ValuedParameter(Prefix='-',Name='p',Delimiter=' ',Value=param_dir)
}
_command = 'sfold.X86_64.LINUX'
_input_handler = '_input_as_string'
def _get_result_paths(self,data):
"""Return a dict of ResultPath objects representing all possible output
"""
result = {}
#list of output files
output_list = ['10structure','10structure_2','Dharmacon_thermo','bp',
'bprob','cdf','fe','loopr','oligo','oligo_f','pdf',
'sample','sample_1000','sirna','sirna_f','sirna_s',
'smfe','sstrand','stability']
for name in output_list:
try:
path = '%s%s.out' % (self.WorkingDir,name)
f = open(path)
f.close()
result[name] = \
ResultPath(Path=path)
except IOError:
stderr.write('path: %s\n' % self.WorkingDir)
stderr.write('File: %s.out not written to result dict\n' % name)
pass
return result
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