Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
parents 769e306b7933
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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
32 import os
33 import struct
34 from optparse import OptionParser
35 from commons.core.parsing.GffParser import GffParser
36 from commons.core.writer.Gff3Writer import Gff3Writer
37
38 LONGSIZE = struct.calcsize('l')
39
40 class FindOverlaps_naif(object):
41
42 def __init__(self, inputRefGff3FileName, inputQueryGff3FileName):
43 self._inputRefGff3FileName = inputRefGff3FileName
44 self._inputQueryGff3FileName = inputQueryGff3FileName
45
46 def close(self):
47 self._iGff3Writer.close()
48
49 def setGff3FileName(self, fileName):
50 self._inputRefGff3FileName = fileName
51
52 def setQueryGff3FileName(self, fileName):
53 self._inputQueryGff3FileName = fileName
54
55 def setOutputGff3FileName(self, outputGff3FileName):
56 if outputGff3FileName != '':
57 self._outputGff3FileName = outputGff3FileName
58 self._iGff3Writer = Gff3Writer(self._outputGff3FileName)
59
60 def run(self):
61 queryParser = GffParser(self._inputQueryGff3FileName, 0)
62 for queryTranscript in queryParser.getIterator():
63 ids = []
64 refParser = GffParser(self._inputRefGff3FileName, 0)
65 for refTranscript in refParser.getIterator():
66 if queryTranscript.overlapWith(refTranscript):
67 ids.append(refTranscript.getTagValue('ID'))
68 if ids:
69 queryTranscript.setTagValue("nbOverlaps", len(ids))
70 queryTranscript.setTagValue("overlapsWith", "--".join(ids))
71 self._iGff3Writer.addTranscript(queryTranscript)
72
73 if __name__ == "__main__":
74 description = "FindOverlapsWithSeveralInterval: Finds overlaps with several query intervals."
75
76 parser = OptionParser(description = description)
77 parser.add_option("-i", "--inputRef", dest="inputRefGff3FileName", action="store", type="string", help="Reference input file [compulsory] [format: file in gff3 format]")
78 parser.add_option("-j", "--inputQuery", dest="inputQueryGff3FileName", action="store", type="string", help="Query input file [compulsory] [format: file in gff3 format]")
79 parser.add_option("-o", "--output", dest="outputGff3FileName", action="store", type="string", help="output file [compulsory] [format: output file in gff3 format]")
80 (options, args) = parser.parse_args()
81
82 iFON = FindOverlaps_naif(options.inputRefGff3FileName, options.inputQueryGff3FileName)
83 iFON.setOutputGff3FileName(options.outputGff3FileName)
84 iFON.run()
85 iFON.close()