comparison SMART/Java/Python/getWigData.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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()