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comparison smart_toolShed/SMART/Java/Python/getNb.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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 """Get the repartition of some elements (# exons per transcripts, # of repetitions of a mapping or # of transcripts in a cluster)"""
32
33 from optparse import OptionParser
34 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
35 from SMART.Java.Python.misc.RPlotter import RPlotter
36 from SMART.Java.Python.misc.Progress import Progress
37 from SMART.Java.Python.misc import Utils
38 from math import *
39
40 if __name__ == "__main__":
41
42 # parse command line
43 description = "Get Nb v1.0.1: Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster. [Category: Visualization]"
44
45 parser = OptionParser(description = description)
46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
48 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in png format]")
49 parser.add_option("-q", "--query", dest="query", action="store", type="string", help="query [compulsory] (# exons, # transcripts) [format: choice (exon, transcript, cluster)]")
50 parser.add_option("-b", "--barplot", dest="barplot", action="store_true", default=False, help="use barplot representation [format: bool] [default: false]")
51 parser.add_option("-x", "--xMax", dest="xMax", action="store", default=None, type="int", help="maximum value on the x-axis to plot [format: int]")
52 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
53 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
54 (options, args) = parser.parse_args()
55
56 if options.query != "exon" and options.query != "transcript" and options.query != "cluster":
57 raise Exception("Do not understand query %s" % (options.query))
58
59 exonDistribution = {}
60 transcriptDistribution = {}
61 clusterDistribution = {}
62
63 transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
64
65 progress = Progress(transcriptContainer.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
66 # count the number of reads
67 for element in transcriptContainer.getIterator():
68 if options.query == "exon":
69 nbExons = element.getNbExons()
70 exonDistribution[nbExons] = exonDistribution.get(nbExons, 0) + 1
71 elif options.query == "transcript":
72 name = element.getName()
73 transcriptDistribution[name] = transcriptDistribution.get(name, 0) + 1
74 elif options.query == "cluster":
75 nbElements = 1 if "nbElements" not in element.getTagNames() else element.getTagValue("nbElements")
76 clusterDistribution[nbElements] = clusterDistribution.get(nbElements, 0) + 1
77 progress.inc()
78 progress.done()
79
80 if options.query == "exon":
81 distribution = exonDistribution
82 elif options.query == "transcript":
83 distribution = {}
84 for name in transcriptDistribution:
85 distribution[transcriptDistribution[name]] = distribution.get(transcriptDistribution[name], 0) + 1
86 elif options.query == "cluster":
87 distribution = clusterDistribution
88
89 outputFileName = options.outputFileName
90 plotter = RPlotter(outputFileName, options.verbosity)
91 plotter.setImageSize(1000, 300)
92 plotter.setFill(0)
93 plotter.setMaximumX(options.xMax)
94 plotter.setBarplot(options.barplot)
95 plotter.addLine(distribution)
96 plotter.plot()
97
98 print "min/avg/med/max: %d/%.2f/%.1f/%d" % (Utils.getMinAvgMedMax(distribution))
99