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comparison SMART/Java/Python/getInfoPerCoverage.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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 """Compare overlap of a transcript list and list of read, and get some info depending on the coverage"""
32
33 import os
34 from optparse import OptionParser
35 from commons.core.parsing.SequenceListParser import *
36 from commons.core.writer.Gff3Writer import *
37 from SMART.Java.Python.mySql.MySqlConnection import *
38 from SMART.Java.Python.structure.TranscriptListsComparator import *
39 from SMART.Java.Python.misc.RPlotter import *
40 from SMART.Java.Python.misc.Progress import *
41
42
43 if __name__ == "__main__":
44
45 # parse command line
46 description = "Get Info per Coverage v1.0.1: Get a list of information clustered by the density of the coverage on a genome. [Category: Personnal]"
47
48 parser = OptionParser(description = description)
49 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
50 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
51 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
52 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]")
53 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in TXT format]")
54 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
55 parser.add_option("-l", "--log", dest="log", action="store", default=None, type="string", help="write a log file [format: bool] [default: false]")
56 (options, args) = parser.parse_args()
57
58 logHandle = None
59 if options.log != None:
60 logHandle = open(options.log, "w")
61
62 transcriptContainer1 = TranscriptContainer(options.inputFileName1, options.format1, options.verbosity)
63 transcriptContainer2 = TranscriptContainer(options.inputFileName2, options.format2, options.verbosity)
64
65 transcriptListComparator = TranscriptListsComparator(logHandle, options.verbosity)
66 transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, 10)
67 transcriptListComparator.getColinearOnly(True)
68 transcriptListComparator.computeOddsPerTranscript(True)
69 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1)
70 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2)
71 transcriptListComparator.compareTranscriptList()
72 transcriptTables = transcriptListComparator.getOutputTables()
73
74 sizesWithIntrons = {}
75 sizesWithoutIntrons = {}
76 nbExons = {}
77 averageSizesWithIntrons = {}
78 averageSizesWithoutIntrons = {}
79 averageNbExons = {}
80 sumSizesWithIntrons = {}
81 sumSizesWithoutIntrons = {}
82 sumSizesNbExons = {}
83 coverages = transcriptListComparator.getOddsPerTranscript()
84
85 progress = Progress(transcriptContainer2.getNbTranscripts(), "Reading transcript file again", options.verbosity)
86 for transcript in transcriptContainer2.getIterator():
87 if transcript.name in coverages:
88 if transcript.getSizeWithIntrons() not in averageSizesWithIntrons:
89 averageSizesWithIntrons[transcript.getSizeWithIntrons()] = coverages[transcript.name]
90 else:
91 averageSizesWithIntrons[transcript.getSizeWithIntrons()] += coverages[transcript.name]
92 if transcript.getSizeWithIntrons() not in sumSizesWithIntrons:
93 sumSizesWithIntrons[transcript.getSizeWithIntrons()] = 1
94 else:
95 sumSizesWithIntrons[transcript.getSizeWithIntrons()] += 1
96 if transcript.getSize() not in averageSizesWithoutIntrons:
97 averageSizesWithoutIntrons[transcript.getSize()] = coverages[transcript.name]
98 else:
99 averageSizesWithoutIntrons[transcript.getSize()] += coverages[transcript.name]
100 if transcript.getSize() not in sumSizesWithoutIntrons:
101 sumSizesWithoutIntrons[transcript.getSize()] = 1
102 else:
103 sumSizesWithoutIntrons[transcript.getSize()] += 1
104 if transcript.getNbExons() not in averageNbExons:
105 averageNbExons[transcript.getNbExons()] = coverages[transcript.name]
106 else:
107 averageNbExons[transcript.getNbExons()] += coverages[transcript.name]
108 if transcript.getNbExons() not in sumSizesNbExons:
109 sumSizesNbExons[transcript.getNbExons()] = 1
110 else:
111 sumSizesNbExons[transcript.getNbExons()] += 1
112 sizesWithIntrons[transcript.name] = (transcript.getSizeWithIntrons(), coverages[transcript.name])
113 sizesWithoutIntrons[transcript.name] = (transcript.getSize(), coverages[transcript.name])
114 nbExons[transcript.name] = (transcript.getNbExons(), coverages[transcript.name])
115 progress.inc()
116 progress.done()
117
118 plotterSizeWithIntrons = RPlotter("%sWithIntrons.png" % (options.output), options.verbosity)
119 plotterSizeWithIntrons.setPoints(True)
120 plotterSizeWithIntrons.setMaximumX(10000)
121 plotterSizeWithIntrons.setMaximumY(1000)
122 plotterSizeWithIntrons.setLog("y")
123 plotterSizeWithIntrons.addLine(sizesWithIntrons)
124 plotterSizeWithIntrons.plot()
125
126 plotterSizeWithoutIntrons = RPlotter("%sWithoutIntrons.png" % (options.output), options.verbosity)
127 plotterSizeWithoutIntrons.setPoints(True)
128 plotterSizeWithoutIntrons.setMaximumX(10000)
129 plotterSizeWithoutIntrons.setMaximumY(1000)
130 plotterSizeWithoutIntrons.setLog("y")
131 plotterSizeWithoutIntrons.addLine(sizesWithoutIntrons)
132 plotterSizeWithoutIntrons.plot()
133
134 plotterNbExons = RPlotter("%sNbExons.png" % (options.output), options.verbosity)
135 plotterNbExons.setPoints(True)
136 plotterNbExons.addLine(nbExons)
137 plotterNbExons.plot()
138
139 for element in averageSizesWithIntrons:
140 averageSizesWithIntrons[element] = int(float(averageSizesWithIntrons[element]) / sumSizesWithIntrons[element])
141 plotterAverageSizeWithIntrons = RPlotter("%sAverageWithIntrons.png" % (options.output), options.verbosity)
142 plotterAverageSizeWithIntrons.setMaximumX(10000)
143 plotterAverageSizeWithIntrons.setMaximumY(1000)
144 plotterAverageSizeWithIntrons.setLog("y")
145 plotterAverageSizeWithIntrons.addLine(averageSizesWithIntrons)
146 plotterAverageSizeWithIntrons.plot()
147 print "min/avg/med/max sizes with introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithIntrons)
148
149 for element in averageSizesWithoutIntrons:
150 averageSizesWithoutIntrons[element] = int(float(averageSizesWithoutIntrons[element]) / sumSizesWithoutIntrons[element])
151 plotterAverageSizeWithoutIntrons = RPlotter("%sAverageWithoutIntrons.png" % (options.output), options.verbosity)
152 plotterAverageSizeWithoutIntrons.setMaximumX(10000)
153 plotterAverageSizeWithoutIntrons.setMaximumY(1000)
154 plotterAverageSizeWithoutIntrons.setLog("y")
155 plotterAverageSizeWithoutIntrons.addLine(averageSizesWithoutIntrons)
156 plotterAverageSizeWithoutIntrons.plot()
157 print "min/avg/med/max sizes without introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithoutIntrons)
158
159 for element in averageNbExons:
160 averageNbExons[element] = int(float(averageNbExons[element]) / sumSizesNbExons[element])
161 plotterAverageNbExons = RPlotter("%sAverageNbExons.png" % (options.output), options.verbosity)
162 plotterAverageNbExons.addLine(averageNbExons)
163 plotterAverageNbExons.plot()
164 print "min/avg/med/max # exons: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageNbExons)
165
166 if options.log:
167 logHandle.close()