Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/changeTagName.py @ 58:5f5c9b74c2dd
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author | m-zytnicki |
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date | Fri, 07 Feb 2014 11:53:36 -0500 |
parents | 769e306b7933 |
children | 783e6ed4eb66 |
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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. # """ Change the name of a tag """ import os import random from optparse import OptionParser from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer from SMART.Java.Python.misc.Progress import Progress from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter from commons.core.writer.Gff3Writer import Gff3Writer if __name__ == "__main__": # parse command line description = "Change Tag Name v1.0.1: Change the name of tag of a list of transcripts. [Category: Data Modification]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]") parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]") parser.add_option("-t", "--tag", dest="tag", action="store", type="string", help="name of the tag to change [compulsory] [format: string]") parser.add_option("-n", "--name", dest="name", action="store", type="string", help="new name for the tag [compulsory] [format: string]") parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]") (options, args) = parser.parse_args() if options.log: logHandle = open("%s.log" % options.outputFileName, "w") # create parser and writer(s) parser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity) tmpFileName = "tmpTranscriptFile%d.gff3" % (random.randint(0, 100000)) writer = Gff3Writer(tmpFileName, options.verbosity) if options.mysql: mysqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity) outputData = {} # process transcripts progress = Progress(parser.getNbTranscripts(), "Printing transcripts %s" % (options.inputFileName), options.verbosity) for transcript in parser.getIterator(): if options.tag in transcript.tags: value = transcript.tags[options.tag] del transcript.tags[options.tag] transcript.tags[options.name] = value writer.addTranscript(transcript) if options.mysql: mysqlWriter.addTranscript(transcript) progress.inc() progress.done() parser.transcriptListParser.close() writer.write() if options.mysql: mysqlWriter.write() os.rename(tmpFileName, options.outputFileName)