Mercurial > repos > yufei-luo > s_mart
view commons/launcher/LaunchRepeatMasker.py @ 18:94ab73e8a190
Uploaded
author | m-zytnicki |
---|---|
date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | |
children |
line wrap: on
line source
#! /usr/bin/env python # Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. from commons.core.checker.CheckerUtils import CheckerUtils from commons.core.utils.FileUtils import FileUtils from commons.core.utils.RepetOptionParser import RepetOptionParser import subprocess class LaunchRepeatMasker(object): def __init__(self,queryFileName="", libFileName ="",sensitivity="", engine="wu", cutOff=225, outputDir = ".",verbosity=0): self._queryFileName = queryFileName self._libFileName = libFileName self._engine = engine self._sensitivity = sensitivity self._cutOff = cutOff self._outputDir = outputDir self._verbosity = verbosity def setAttributesFromCmdLine(self): description = "LaunchRepeatMasker runs the RepeatMasker program ." parser = RepetOptionParser(description = description) parser.add_option("-q", "--query", dest="queryFileName", default = None, action="store", type="string", help="input query file [compulsory] [format: fasta]") parser.add_option("-l", "--libFileName", dest="libFileName", default = None, action="store", type="string", help="custom library [optional]") parser.add_option("-n", "--outputDir", dest="outputDir", default=".", action="store", type="string", help="outputDir (default : current directory) [optional] ") parser.add_option("-c", "--cutOff", dest="cutOff", default=225, action="store", type="int", help="Sets cutoff score for masking repeats when using -lib (default 225) [optional] ") parser.add_option("-e", "--engine", dest="engine", default = "wu", action="store", type="string", help="engine [optional] ") parser.add_option("-u", "--sensitivity", dest="sensitivity", default = "", action="store", type="string", help="sensitivity can be s, q, qq[optional] ") parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ") (options, args) = parser.parse_args() self._setAttributesFromOptions(options) def _setAttributesFromOptions(self, options): self._queryFileName = options.queryFileName self._libFileName = options.libFileName self._outputDir = options.outputDir self._engine = options.engine self._sensitivity = options.sensitivity self._cutOff = options.cutOff self._verbosity = options.verbosity def checkOptions(self): if self._queryFileName != "": if not FileUtils.isRessourceExists(self._queryFileName): raise Exception("ERROR: Query file: %s does not exist!" % self._queryFileName) else: raise Exception("ERROR: No specified --query option!") def run(self): if not CheckerUtils.isExecutableInUserPath("RepeatMasker") : print "ERROR: RepeatMasker must be in your path" else: self.checkOptions() engine = "" if self._engine == "wu": engine = "-e wublast" elif self._engine == "cm": engine = "-e crossmatch" sensitivity = "" if self._sensitivity: sensitivity = "-%s" % self._sensitivity libFileName = "" if self._libFileName != "": libFileName = "-lib %s" % self._libFileName cmd = "RepeatMasker %s -dir %s -pa 1 -gccalc -no_is -nolow %s %s %s" % (self._queryFileName,self._outputDir,engine,sensitivity,libFileName) cmd = cmd.split() if self._verbosity>0: print("Running RepeatMasker with following commands : %s" %cmd) process = subprocess.Popen(cmd, stdout=subprocess.PIPE,stderr = subprocess.PIPE) # process.wait() output= process.communicate() if self._verbosity>0: print("".join(output)) return process.returncode if __name__ == "__main__": iLaunchRepeatMasker = LaunchRepeatMasker() iLaunchRepeatMasker.setAttributesFromCmdLine() iLaunchRepeatMasker.run()