/usr/lib/python2.7/dist-packages/cogent/app/carnac.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 90 91 92 93 94 | #!/usr/bin/env python
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter,FlagParameter,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 Carnac(CommandLineApplication):
"""Application controller for Carnac RNAfolding application
Info at:
http://bioinfo.lifl.fr/carnac/index.html
Options:
-a Inhibit the energy correction that is automatically
performed to create the initial set of potential
stems. By default, the energy correction depends of the
GC percentage of each sequence.
-c Eliminate sequences that are too similar. The similarity
treshold is 98%.
-h Add hairpins that are present only in one sequence to
the initial set of potential stems (may be time and space
demanding).
"""
#Limitation
#if -c is turned on and file is deleted error in file handling in _get_result_paths
_parameters = {
'-c':FlagParameter(Prefix='-',Name='c',Value=False),
'-a':FlagParameter(Prefix='-',Name='a'),
'-h':FlagParameter(Prefix='-',Name='h')}
_command = 'carnac'
_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 of the application is called on
Carnac produces it's output to a .ct, .eq, to the location of input file
and .out files located in the same folder as the program is run from.
graph and align file is also created.
You always get back: StdOut,StdErr, and ExitStatus
"""
result={}
name_counter = 0
ones='00'
tens='0'
count=''
if not isinstance(data,list):
#means data is file
path=str(data)
data=open(data).readlines()
else: #data input as lines
#path=''.join([self.WorkingDir,self._input_filename.split('/')[-1]])
path = ''.join(['/tmp/', self._input_filename.split('/')[-1]])
for item in data:
if item.startswith('>'):
name_counter += 1
if name_counter < 10:
count=ones
if name_counter > 9:
count=tens
if name_counter > 99:
count=''
name = item.strip('>\n')
else:
nr=name_counter
result['ct%d' % nr] =\
ResultPath(Path=('%s%s%d.ct' % (path,count,nr)))
result['eq%d' % nr] =\
ResultPath(Path=('%s%s%d.eq' % (path,count,nr)))
result['out_seq%d' % nr] = \
ResultPath(Path=(''.join([self.WorkingDir,'Z_%s%d.%s.out'% \
(count,nr,name)])))
result['graph'] =\
ResultPath(Path=(self.WorkingDir+'graph.out'))
result['align'] =\
ResultPath(Path=(self.WorkingDir+'alignment.out'))
return result
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