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comparison smart_toolShed/SMART/Java/Python/ComputeCoverage.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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-1:000000000000 0:e0f8dcca02ed
1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2011
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 import os, random
32 from optparse import OptionParser, OptionGroup
33 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
34 from SMART.Java.Python.misc.Progress import Progress
35 from commons.core.writer.Gff3Writer import Gff3Writer
36
37
38 class CoverageComputer(object):
39
40 def __init__(self, verbosity = 0):
41 self.verbosity = verbosity
42 self.queryReader = None
43 self.referenceReader = None
44 self.outputWriter = None
45 self.introns = False
46 self.nbNucleotides = 0
47 self.nbCovered = 0
48
49 def setInputQueryFile(self, fileName, format):
50 self.queryReader = TranscriptContainer(fileName, format, self.verbosity-1)
51
52 def setInputReferenceFile(self, fileName, format):
53 self.referenceReader = TranscriptContainer(fileName, format, self.verbosity-1)
54
55 def includeIntrons(self, boolean):
56 self.introns = boolean
57
58 def setOutputFileName(self, fileName, title="S-MART", feature="transcript", featurePart="exon"):
59 self.outputWriter = Gff3Writer(fileName, self.verbosity-1)
60 self.outputWriter.setTitle(title)
61 self.outputWriter.setFeature(feature)
62 self.outputWriter.setFeaturePart(featurePart)
63
64 def readReference(self):
65 self.coveredRegions = {}
66 progress = Progress(self.referenceReader.getNbTranscripts(), "Reading reference file", self.verbosity-1)
67 for transcript in self.referenceReader.getIterator():
68 chromosome = transcript.getChromosome()
69 if chromosome not in self.coveredRegions:
70 self.coveredRegions[chromosome] = {}
71 if self.introns:
72 transcript.removeExons()
73 for exon in transcript.getExons():
74 for position in range(exon.getStart(), exon.getEnd()+1):
75 self.coveredRegions[chromosome][position] = 1
76 progress.inc()
77 progress.done()
78
79 def readQuery(self):
80 progress = Progress(self.queryReader.getNbTranscripts(), "Reading query file", self.verbosity-1)
81 for transcript in self.queryReader.getIterator():
82 progress.inc()
83 chromosome = transcript.getChromosome()
84 if chromosome not in self.coveredRegions:
85 continue
86 if self.introns:
87 transcript.removeExons()
88 for exon in transcript.getExons():
89 for position in range(exon.getStart(), exon.getEnd()+1):
90 self.nbNucleotides += 1
91 self.nbCovered += self.coveredRegions[chromosome].get(position, 0)
92 progress.done()
93
94 def write(self):
95 progress = Progress(self.queryReader.getNbTranscripts(), "Writing output file", self.verbosity-1)
96 for transcript in self.queryReader.getIterator():
97 chromosome = transcript.getChromosome()
98 if self.introns:
99 transcript.removeExons()
100 size = transcript.getSize()
101 coverage = 0
102 for exon in transcript.getExons():
103 for position in range(exon.getStart(), exon.getEnd()+1):
104 coverage += self.coveredRegions[chromosome].get(position, 0)
105 transcript.setTagValue("coverage", 0 if size == 0 else float(coverage) / size * 100)
106 self.outputWriter.addTranscript(transcript)
107 progress.inc()
108 progress.done()
109
110 def sumUp(self):
111 print "%d nucleotides in query, %d (%.f%%) covered" % (self.nbNucleotides, self.nbCovered, 0 if self.nbNucleotides == 0 else float(self.nbCovered) / self.nbNucleotides * 100)
112
113 def run(self):
114 self.readReference()
115 self.readQuery()
116 if self.outputWriter != None:
117 self.write()
118 self.sumUp()
119
120
121 if __name__ == "__main__":
122
123 # parse command line
124 description = "Compute Coverage v1.0.1: Compute the coverage of a set with respect to another set. [Category: Personal]"
125
126 parser = OptionParser(description = description)
127 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input query file [compulsory] [format: file in transcript format given by -f]")
128 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of the first file [compulsory] [format: transcript file format]")
129 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input reference file [compulsory] [format: file in transcript format given by -f]")
130 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of the second file [compulsory] [format: transcript file format]")
131 parser.add_option("-t", "--introns", dest="introns", action="store_true", default=False, help="also include introns [format: boolean] [default: false]")
132 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in GFF3 format]")
133 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", type="int", help="trace level [default: 1] [format: int]")
134 (options, args) = parser.parse_args()
135
136 computer = CoverageComputer(options.verbosity)
137 computer.setInputQueryFile(options.inputFileName1, options.format1)
138 computer.setInputReferenceFile(options.inputFileName2, options.format2)
139 computer.includeIntrons(options.introns)
140 computer.setOutputFileName(options.outputFileName)
141 computer.run()
142