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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 from optparse import OptionParser
+ − 32 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 33 from commons.core.parsing.WigParser import WigParser
+ − 34 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 35 from SMART.Java.Python.misc.Progress import Progress
+ − 36
+ − 37
+ − 38 if __name__ == "__main__":
+ − 39
+ − 40 # parse command line
+ − 41 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]"
+ − 42
+ − 43 parser = OptionParser(description = description)
+ − 44 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 45 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
+ − 46 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
+ − 47 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]")
+ − 48 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 49 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
+ − 50 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 51 (options, args) = parser.parse_args()
+ − 52
+ − 53 # create parsers and writers
+ − 54 transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
+ − 55 wigParser = WigParser(options.wig)
+ − 56 writer = Gff3Writer(options.outputFileName, options.verbosity)
+ − 57 wigParser.setStrands(options.strands)
+ − 58
+ − 59 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
+ − 60 for transcript in transcriptParser.getIterator():
+ − 61 values = transcript.extractWigData(wigParser)
+ − 62 if options.strands:
+ − 63 values = values[transcript.getDirection()]
+ − 64 transcript.setTagValue(options.tag, str(float(sum(values)) / len(values)))
+ − 65 writer.addTranscript(transcript)
+ − 66 progress.inc()
+ − 67 progress.done()
