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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
