annotate smart_toolShed/SMART/Java/Python/getWigData.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
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from optparse import OptionParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from commons.core.parsing.WigParser import WigParser
from commons.core.writer.Gff3Writer import Gff3Writer
from SMART.Java.Python.misc.Progress import Progress


if __name__ == "__main__":
    
    # parse command line
    description = "Get WIG Data v1.0.1: Compute the average data for some genomic coordinates using WIG files (thus covering a large proportion of the genome) and update a tag. [Category: WIG Tools]"

    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("-w", "--wig",         dest="wig",            action="store",                     type="string", help="wig file name [compulsory] [format: file in WIG format]")    
    parser.add_option("-t", "--tag",         dest="tag",            action="store",                     type="string", help="choose a tag name to write the wig information to output file [compulsory] [format: file in WIG 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("-s", "--strands",     dest="strands",        action="store_true", default=False,                help="consider both strands separately [format: boolean] [default: False]")    
    parser.add_option("-v", "--verbosity",   dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    # create parsers and writers
    transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
    wigParser        = WigParser(options.wig)
    writer           = Gff3Writer(options.outputFileName, options.verbosity)
    wigParser.setStrands(options.strands)
    
    progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
    for transcript in transcriptParser.getIterator():
        values = transcript.extractWigData(wigParser)
        if options.strands:
            values = values[transcript.getDirection()]
        transcript.setTagValue(options.tag, str(float(sum(values)) / len(values)))
        writer.addTranscript(transcript)
        progress.inc()
    progress.done()