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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
+ − 32 from optparse import OptionParser
+ − 33 from commons.core.parsing.FastaParser import FastaParser
+ − 34 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 35 from SMART.Java.Python.misc.Progress import Progress
+ − 36 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 37 from SMART.Java.Python.misc.Utils import *
+ − 38
+ − 39
+ − 40 class GetGenomeCoverage(object):
+ − 41
+ − 42 def __init__(self, verbosity = 1):
+ − 43 self.verbosity = verbosity
+ − 44 self.inputContainer = None
+ − 45 self.referenceParser = None
+ − 46 self.outputFileName = None
+ − 47 self.genomeSize = None
+ − 48 self.coverage = {}
+ − 49 self.distribution = {}
+ − 50
+ − 51
+ − 52 def setInputFile(self, fileName, format):
+ − 53 self.inputContainer = TranscriptContainer(fileName, format, self.verbosity)
+ − 54
+ − 55
+ − 56 def setOutputFile(self, fileName):
+ − 57 self.outputFileName = fileName
+ − 58
+ − 59
+ − 60 def setReference(self, fileName):
+ − 61 self.referenceParser = FastaParser(fileName, self.verbosity)
+ − 62
+ − 63
+ − 64 def getReferenceSizes(self):
+ − 65 self.genomeSize = 0
+ − 66 for chromosome in self.referenceParser.getRegions():
+ − 67 self.genomeSize += self.referenceParser.getSizeOfRegion(chromosome)
+ − 68
+ − 69
+ − 70 def getCoverage(self):
+ − 71 progress = Progress(self.inputContainer.getNbTranscripts(), "Reading reads", self.verbosity)
+ − 72 for transcript in self.inputContainer.getIterator():
+ − 73 chromosome = transcript.getChromosome()
+ − 74 if chromosome not in self.coverage:
+ − 75 self.coverage[chromosome] = {}
+ − 76 for exon in transcript.getExons():
+ − 77 for pos in range(exon.getStart(), exon.getEnd() + 1):
+ − 78 if pos not in self.coverage[chromosome]:
+ − 79 self.coverage[chromosome][pos] = 1
+ − 80 else:
+ − 81 self.coverage[chromosome][pos] += 1
+ − 82 progress.inc()
+ − 83 progress.done()
+ − 84
+ − 85
+ − 86 def getDistribution(self):
+ − 87 nbNucleotides = sum([len(self.coverage[chromosome].keys()) for chromosome in self.coverage])
+ − 88 progress = Progress(nbNucleotides, "Building distribution", self.verbosity)
+ − 89 for chromosome in self.coverage:
+ − 90 for num in self.coverage[chromosome].values():
+ − 91 if num not in self.distribution:
+ − 92 self.distribution[num] = 1
+ − 93 else:
+ − 94 self.distribution[num] += 1
+ − 95 progress.inc()
+ − 96 progress.done()
+ − 97 self.distribution[0] = self.genomeSize - nbNucleotides
+ − 98
+ − 99
+ − 100 def plotDistribution(self):
+ − 101 plotter = RPlotter(self.outputFileName, self.verbosity)
+ − 102 plotter.setFill(0)
+ − 103 plotter.addLine(self.distribution)
+ − 104 plotter.plot()
+ − 105 print "min/avg/med/max reads per base: %d/%.2f/%.1f/%d" % getMinAvgMedMax(self.distribution)
+ − 106
+ − 107
+ − 108 def run(self):
+ − 109 self.getReferenceSizes()
+ − 110 self.getCoverage()
+ − 111 self.getDistribution()
+ − 112 self.plotDistribution()
+ − 113
+ − 114
+ − 115 if __name__ == "__main__":
+ − 116
+ − 117 # parse command line
+ − 118 description = "Plot Genome Coverage v1.0.1: Get the coverage of a genome. [Category: Personal]"
+ − 119
+ − 120 parser = OptionParser(description = description)
+ − 121 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="reads file [compulsory] [format: file in transcript format given by -f]")
+ − 122 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
+ − 123 parser.add_option("-r", "--reference", dest="reference", action="store", type="string", help="sequences file [compulsory] [format: file in FASTA format]")
+ − 124 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
+ − 125 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 126 (options, args) = parser.parse_args()
+ − 127
+ − 128 getGenomeCoverage = GetGenomeCoverage(options.verbosity)
+ − 129 getGenomeCoverage.setInputFile(options.inputFileName, options.format)
+ − 130 getGenomeCoverage.setOutputFile(options.outputFileName)
+ − 131 getGenomeCoverage.setReference(options.reference)
+ − 132 getGenomeCoverage.run()
