Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/splitByTag.py @ 47:b6481845eb0d
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author | m-zytnicki |
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date | Mon, 30 Sep 2013 05:51:28 -0400 |
parents | 769e306b7933 |
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#! /usr/bin/env python # # Copyright INRA-URGI 2009-2010 # # 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. # """Read a file and split it into several, depending on a tag""" import os from optparse import OptionParser from SMART.Java.Python.structure.TranscriptContainer import * from commons.core.writer.Gff3Writer import * from SMART.Java.Python.misc.Progress import * from SMART.Java.Python.misc import Utils if __name__ == "__main__": # parse command line description = "Split By Tag v1.0.1: Read a file and split it into several, depending on a tag. [Category: Personnal]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]") parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]") parser.add_option("-t", "--tag", dest="tag", action="store", type="string", help="tag on which the split is made [compulsory] [format: string]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in CSV format]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") (options, args) = parser.parse_args() transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity) writers = dict() progress = Progress(transcriptContainer.getNbTranscripts(), "Reading file %s" % (options.inputFileName), options.verbosity) for transcript in transcriptContainer.getIterator(): value = transcript.getTagValue(options.tag) if value == None: value = "noTag" value = str(value).replace(" ", "_").title() if value not in writers: writers[value] = Gff3Writer("%s.gff3" % (os.path.join(options.outputFileName, value))) writers[value].addTranscript(transcript) progress.inc() progress.done()