/usr/lib/python2.7/dist-packages/cogent/app/unafold.py is in python-cogent 1.9-9.
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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 | #!/usr/bin/env python
"""Application controller for unafold 3.2, hybrid_ss_min application, package
Rest fo unafold package might be added at a later time
"""
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
Parameters
__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 hybrid_ss_min(CommandLineApplication):
"""Application controller for hybrid_ss_min application
Computes a minimum energy folding for a RNA or DNA sequence
"""
#not all options supported here!
#left out: -n,-d,-r,-f,-I,-q,-c,-b and all obscure options
_parameters = {
't':ValuedParameter(Prefix='-',Name='t',Value=None,Delimiter=' '),
'T':ValuedParameter(Prefix='-',Name='T',Value=None,Delimiter=' '),
'i':ValuedParameter(Prefix='-',Name='i',Value=None,Delimiter=' '),
's':ValuedParameter(Prefix='-',Name='s',Value=None,Delimiter=' '),
'o':ValuedParameter(Prefix='-',Name='o',Value=None,Delimiter=' '),
'N':ValuedParameter(Prefix='-',Name='N',Value=None,Delimiter=' '),
'M':ValuedParameter(Prefix='-',Name='M',Value=None,Delimiter=' '),
'p':ValuedParameter(Prefix='-',Name='p',Value=None,Delimiter=' '),
'E':FlagParameter(Prefix='-',Name='E'),
'F':ValuedParameter(Prefix='-',Name='F',Value=None,Delimiter=' '),
'm':ValuedParameter(Prefix='-',Name='m',Value=None,Delimiter=' ')}
_command = 'hybrid-ss-min'
_input_handler = '_input_as_string'
def _get_result_paths(self,data):
"""Return a dict of ResultPath objects representing all possible output
This dictionary will have keys based
on the name that you'd like to access the file by in the
CommandLineAppResult object that will be created, and the values
which are ResultPath objects."""
result = {}
#UNAfold default values
start_tmp = 37
step = 1
end_tmp = 38
if isinstance(data,list):
filename=self._input_filename.split('/')[-1]
else:
filename=data.split('/')[-1]
result['ct']= \
ResultPath(Path=(self.WorkingDir+filename+'.ct'))
result['dG'] = \
ResultPath(Path=(self.WorkingDir+filename+'.dG'))
result['run'] = \
ResultPath(Path=(self.WorkingDir+filename+'.run'))
#if temp interval is not default it will result in more output-files
#one for every temp
if self.Parameters['t'].Value is not None:
start_tmp = self.Parameters['t'].Value
if self.Parameters['T'].Value is not None:
end_tmp = self.Parameters['T'].Value + 1
if self.Parameters['i'].Value is not None:
step = self.Parameters['i'].Value
for i in range(start_tmp,end_tmp,step):
temp = str(i)
result['plot_%d' % i]= \
ResultPath(Path=(self.WorkingDir+filename+'.'+temp+'.plot'))
result['ext_%d' % i]= \
ResultPath(Path=(self.WorkingDir+filename+'.'+temp+'.ext'))
return result
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