Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/Java/Python/changeTagName.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/Java/Python/changeTagName.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,90 @@ +#! /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)