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comparison smart_toolShed/SMART/Java/Python/getElement.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 #! /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 """Get the first element (exon / intron) from a list of transcripts"""
32
33 import os
34 from optparse import OptionParser
35 from commons.core.writer.Gff3Writer import *
36 from SMART.Java.Python.structure.TranscriptContainer import *
37 from SMART.Java.Python.misc.Progress import *
38
39
40 if __name__ == "__main__":
41
42 # parse command line
43 description = "Get Element v1.0.1: Get the first element (exon / intron) from a list of transcripts. [Category: Personnal]"
44
45 parser = OptionParser(description = description)
46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
48 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
49 parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]")
50 parser.add_option("-t", "--type", dest="type", action="store", type="string", help="type of the element [format: choice (exon, intron)]")
51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
52 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
53 (options, args) = parser.parse_args()
54
55 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
56 writer = Gff3Writer(options.outputFileName, options.verbosity)
57 sqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
58
59 nbLines = parser.getNbTranscripts()
60 print "%i lines found" % (nbLines)
61
62 # treat transcripts
63 nbWritten = 0
64 nbUsed = 0
65 progress = Progress(nbLines, "Analyzing transcripts of " + options.inputFileName, options.verbosity)
66 for transcript in parser.getIterator():
67
68 outTranscript = Transcript()
69 outTranscript.setName(transcript.getName())
70 outTranscript.setDirection(transcript.getDirection())
71 outTranscript.setChromosome(transcript.getChromosome())
72
73 if options.type == "exon":
74 if len(transcript.getExons()) > 1:
75 transcript.sortExons()
76 outTranscript.setStart(transcript.getExons()[0].getStart())
77 outTranscript.setEnd(transcript.getExons()[0].getEnd())
78 writer.addTranscript(outTranscript)
79 if options.mysql:
80 sqlWriter.addTranscript(transcript)
81 nbWritten += 1
82 nbUsed += 1
83 elif options.type == "intron":
84 used = False
85 for intron in transcript.getIntrons():
86 used = True
87 thisTranscript = Transcript()
88 thisTranscript.copy(outTranscript)
89 thisTranscript.setStart(intron.getStart())
90 thisTranscript.setEnd(intron.getEnd())
91 writer.addTranscript(thisTranscript)
92 if options.mysql:
93 sqlWriter.addTranscript(transcript)
94 nbWritten += 1
95 if used:
96 nbUsed += 1
97 else:
98 sys.exit("Cannot understan type %s" % (options.type))
99 progress.inc()
100 progress.done()
101
102 if options.mysql:
103 sqlWriter.write()
104
105 print "nb sequences used: %d" % (nbUsed)
106 print "nb elements used: %d" % (nbWritten)