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comparison smart_toolShed/SMART/Java/Python/getExons.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 zeroBaseToOneBaseConvertor = (lambda x: x - 1 if x > 0 else x)
38
39 class GetExons(object):
40
41 def __init__(self, verbosity):
42 self.verbosity = verbosity
43 self.selection = False
44
45 def setInputFile(self, fileName, format):
46 chooser = ParserChooser(self.verbosity)
47 chooser.findFormat(format)
48 self.parser = chooser.getParser(fileName)
49
50 def setSelection(self, selection):
51 if selection == None:
52 return
53 self.selection = True
54 self.selectionItems = []
55 self.selectionIntervals = []
56 for part in selection.split(","):
57 try:
58 splittedPart = map(int, part.split(".."))
59 except Exception:
60 raise Exception("Elements '" + splittedPart + "' of selection '" + selection + "' do no seem to be integers!")
61 if len(splittedPart) == 1:
62 self.selectionItems.append(splittedPart[0])
63 elif len(splittedPart) == 2:
64 self.selectionIntervals.append((splittedPart[0], splittedPart[1]))
65 else:
66 raise Exception("Cannot parse elements '" + splittedPart + "' of selection '" + selection + "'!")
67
68 def getSelectionExonIndices(self, nbExons):
69 if not self.selection:
70 return range(nbExons)
71 indices = []
72 for item in self.selectionItems:
73 indices.append(range(nbExons)[zeroBaseToOneBaseConvertor(item)])
74 for start, end in self.selectionIntervals:
75 start, end = map(zeroBaseToOneBaseConvertor, (start, end))
76 if end > 0:
77 end += 1
78 indices.extend(range(nbExons)[start:end])
79 return indices
80
81 def setOutputFile(self, fileName):
82 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
83
84 def run(self):
85 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
86 nbExons = 0
87 for cpt1, transcript in enumerate(self.parser.getIterator()):
88 selectedExons = self.getSelectionExonIndices(transcript.getNbExons())
89 transcript.sortExons()
90 for cpt2, exon in enumerate(transcript.getExons()):
91 if cpt2 not in selectedExons:
92 continue
93 exonTranscript = Transcript()
94 exonTranscript.copy(exon)
95 if "Parent" in exonTranscript.tags:
96 del exonTranscript.tags["Parent"]
97 exonTranscript.tags["feature"] = "transcript"
98 if "ID" not in exonTranscript.tags or exonTranscript.tags["ID"] == "unnamed transcript":
99 exonTranscript.tags["ID"] = "exon_%d-%d" % (cpt1+1, cpt2+1)
100 if exonTranscript.getName() == "unnamed transcript":
101 exonTranscript.setName("exon_%d-%d" % (cpt1+1, cpt2+1))
102 self.writer.addTranscript(exonTranscript)
103 nbExons += 1
104 progress.inc()
105 self.writer.write()
106 self.writer.close()
107 progress.done()
108 if self.verbosity > 1:
109 print "%d transcripts read" % (self.parser.getNbTranscripts())
110 print "%d exons written" % (nbExons)
111
112 if __name__ == "__main__":
113
114 description = "Get Exons v1.0.1: Get the exons of a set of transcripts. [Category: Data Modification]"
115
116 parser = OptionParser(description = description)
117 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
118 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
119 parser.add_option("-s", "--select", dest="select", action="store", default=None, type="string", help="select some of the exons (like '1,2,5..-3,-1') [format: string]")
120 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
121 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
122 (options, args) = parser.parse_args()
123
124 ge = GetExons(options.verbosity)
125 ge.setInputFile(options.inputFileName, options.format)
126 ge.setSelection(options.select)
127 ge.setOutputFile(options.outputFileName)
128 ge.run()