Mercurial > repos > yufei-luo > s_mart
diff commons/launcher/LaunchRepeatMasker.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/launcher/LaunchRepeatMasker.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,113 @@ +#! /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() \ No newline at end of file