decoyfasta_py.defunct.py

#!/usr/bin/env python
"""
Copyright (c) 2010 Christian Fufezan

This file is part of Proteomatic.

Proteomatic is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

Proteomatic is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with Proteomatic.  If not, see <http://www.gnu.org/licenses/>.
"""

import sys, os

sys.path.append('./include/python')
import proteomatic


class DecoyFasta(proteomatic.ProteomaticScript):
    def run(self):
        if 'outputDatabase' in self.output.keys():
            print("Creating taget/decoy database... \n")
            databases = " ".join(["\"{0}\"".format(x) for x in self.input['databases']])
            opts = {
            '--output':         self.output['outputDatabase'],
            '--method':         self.param['targetDecoyMethod'],
            '--decoyFormat':    self.param['decoyEntryPrefix'],
            '--targetFormat':   self.param['targetEntryPrefix'], 
            '--keepStart':      self.param['targetDecoyKeepStart'],
            '--keepEnd':        self.param['targetDecoyKeepEnd']
            }
            command = self.binaryPath('ptb.decoyfasta') + ' '
            for fl, fi in opts.items():
                command += fl + ' "' + str(fi) + '" '
            command += databases
            os.system(command)
            print("done...")
            
if __name__ == '__main__':
    script = DecoyFasta()