Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/plotGenomeCoverage.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 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()