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comparison smart_toolShed/SMART/Java/Python/getIntrons.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 from optparse import OptionParser
32 from commons.core.parsing.ParserChooser import ParserChooser
33 from commons.core.writer.TranscriptWriter import TranscriptWriter
34 from SMART.Java.Python.structure.Transcript import Transcript
35 from SMART.Java.Python.misc.Progress import Progress
36
37 class GetIntrons(object):
38
39 def __init__(self, verbosity):
40 self.verbosity = verbosity
41
42 def setInputFile(self, fileName, format):
43 chooser = ParserChooser(self.verbosity)
44 chooser.findFormat(format)
45 self.parser = chooser.getParser(fileName)
46
47 def setOutputFile(self, fileName):
48 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
49
50 def run(self):
51 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
52 nbIntrons = 0
53 for cpt1, transcript in enumerate(self.parser.getIterator()):
54 for cpt2, intron in enumerate(transcript.getIntrons()):
55 intronTranscript = Transcript()
56 intronTranscript.copy(intron)
57 if "Parent" in intronTranscript.tags:
58 del intronTranscript.tags["Parent"]
59 intronTranscript.tags["feature"] = "transcript"
60 if "ID" not in intronTranscript.tags or intronTranscript.tags["ID"] == "unnamed transcript":
61 intronTranscript.tags["ID"] = "intron_%d-%d" % (cpt1+1, cpt2+1)
62 if intronTranscript.getName() == "unnamed transcript":
63 intronTranscript.setName("intron_%d-%d" % (cpt1+1, cpt2+1))
64 self.writer.addTranscript(intronTranscript)
65 nbIntrons += 1
66 progress.inc()
67 self.writer.write()
68 self.writer.close()
69 progress.done()
70 if self.verbosity > 1:
71 print "%d transcripts read" % (self.parser.getNbTranscripts())
72 print "%d introns written" % (nbIntrons)
73
74
75 if __name__ == "__main__":
76
77 description = "Get Introns v1.0.1: Get the introns of a set of transcripts. [Category: Data Modification]"
78
79 parser = OptionParser(description = description)
80 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
81 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
82 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
83 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
84 (options, args) = parser.parse_args()
85
86 gi = GetIntrons(options.verbosity)
87 gi.setInputFile(options.inputFileName, options.format)
88 gi.setOutputFile(options.outputFileName)
89 gi.run()