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comparison SMART/Java/Python/getWigDistance.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 """
32 Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
33 """
34
35 from optparse import OptionParser
36 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
37 from commons.core.parsing.WigParser import WigParser
38 from SMART.Java.Python.misc.Progress import Progress
39 from SMART.Java.Python.misc.RPlotter import RPlotter
40
41
42 if __name__ == "__main__":
43
44 # parse command line
45 description = "Get WIG Data v1.0.2: Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome). [Category: WIG Tools]"
46
47 parser = OptionParser(description = description)
48 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
49 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
50 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
51 parser.add_option("-d", "--distance", dest="distance", action="store", default=1000, type="int", help="distance around position [compulsory] [format: int] [default: 1000]")
52 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
53 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
54 parser.add_option("-a", "--default", dest="defaultValue", action="store", default=0.0, type="float", help="default value (when value is NA) [default: 0.0] [format: float]")
55 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="use log scale for y-axis [format: boolean] [default: False]")
56 parser.add_option("-k", "--keep", dest="keep", action="store_true", default=False, help="keep temporary files [format: boolean] [default: False]")
57 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
58 (options, args) = parser.parse_args()
59
60 # create parsers and writers
61 transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
62 wigParser = WigParser(options.wig)
63 wigParser.setStrands(options.strands)
64 wigParser.setDefaultValue(options.defaultValue)
65
66 # allocate data
67 strands = (1, -1) if options.strands else (1, )
68 values = {}
69 for strand in strands:
70 values[strand] = dict([(i, 0.0) for i in range(-options.distance, options.distance+1)])
71
72 # read transcripts
73 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
74 for transcript in transcriptParser.getIterator():
75 transcript.removeExons()
76 transcript.restrictStart(2)
77 transcript.extendStart(options.distance)
78 transcript.extendEnd(options.distance-1)
79 theseValues = transcript.extractWigData(wigParser)
80 if len(strands) == 1:
81 theseValues = {1: theseValues}
82 for strand in strands:
83 if len(theseValues[strand]) < 2 * options.distance + 1:
84 theseValues[strand] = [options.defaultValue] * (2 * options.distance + 1 - len(theseValues[strand])) + theseValues[strand]
85 if len(theseValues[strand]) != 2 * options.distance + 1:
86 raise Exception("Got something wrong with the size of the WIG data concerning %s: %d found instead of %d" % (transcript, len(theseValues[strand]), 2 * options.distance + 1))
87 for i in range(-options.distance, options.distance+1):
88 values[strand][i] += theseValues[strand][i + options.distance]
89 progress.inc()
90 progress.done()
91
92 for strand in strands:
93 for i in range(-options.distance, options.distance+1):
94 values[strand][i] /= transcriptParser.getNbTranscripts() * strand
95
96 # draw plot
97 plotter = RPlotter(options.outputFileName, options.verbosity, options.keep)
98 plotter.setXLabel("Distance")
99 plotter.setYLabel("WigValue")
100 for strand in strands:
101 plotter.addLine(values[strand])
102 if options.log:
103 plotter.setLog("y")
104 plotter.plot()
105