annotate smart_toolShed/SMART/Java/Python/splitByTag.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /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
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# "http://www.cecill.info".
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"""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()