comparison SMART/Java/Python/findTss.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 """Find TSS from short reads"""
32 import os
33 from optparse import OptionParser
34 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
36 from commons.core.writer.Gff3Writer import Gff3Writer
37
38 if __name__ == "__main__":
39
40 # parse command line
41 description = "Find TSS v1.0.1: Find the transcription start site of a list of transcripts. [Category: Merge]"
42
43 parser = OptionParser(description = description)
44 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
45 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
46 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
47 parser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False, help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
48 parser.add_option("-d", "--distance", dest="distance", action="store", default=10, type="int", help="distance between two reads to mark the same TSS [format: int] [default: 10]")
49 parser.add_option("-e", "--colinear", dest="colinear", action="store_true", default=False, help="group by strand [format: bool] [default: false]")
50 parser.add_option("-c", "--csv", dest="csv", action="store", default=None, type="string", help="output a CSV file in the given path [format: output file in Excel format]")
51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
52 (options, args) = parser.parse_args()
53
54 transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
55 transcriptListComparator = TranscriptListsComparator(None, options.verbosity)
56 transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, 1)
57 transcriptListComparator.setMaxDistance(options.distance)
58 transcriptListComparator.aggregate(True)
59 transcriptListComparator.computeOdds(True)
60 transcriptListComparator.getColinearOnly(options.colinear)
61 transcriptListComparator.setNormalization(options.normalize)
62 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
63 transcriptListComparator.setOutputWriter(Gff3Writer(options.output, options.verbosity))
64 transcriptListComparator.compareTranscriptListSelfMerge()
65
66 if options.csv != None:
67 csvResults = transcriptListComparator.getOddsPerTranscript()
68 csvFile = open(options.csv, "w")
69 csvFile.write("Number,Transcript\n")
70 for number in sorted(list(set(csvResults.values()))):
71 csvFile.write("%d," % (number))
72 for name in csvResults:
73 if csvResults[name] == number:
74 csvFile.write("%s " % (name))
75 csvFile.write("\n")
76 csvFile.close()
77