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comparison commons/core/parsing/MapParser.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 import re
31 import sys
32 from SMART.Java.Python.structure.Mapping import Mapping
33 from commons.core.parsing.MapperParser import MapperParser
34 from SMART.Java.Python.structure.SubMapping import SubMapping
35 from SMART.Java.Python.misc import Utils
36 from SMART.Java.Python.structure.Transcript import Transcript
37 from commons.core.parsing.TranscriptListParser import TranscriptListParser
38
39
40 class MapParser(TranscriptListParser):
41 """A class that parses the repet .map files"""
42
43 def __init__(self, fileName, verbosity = 0):
44 self._lineParseRe = re.compile(r"(?P<seqName>\w+)\s(?P<chrName>\w+)\s(?P<sStart>\d+)\s(?P<sEnd>\d+)")
45 TranscriptListParser.__init__(self, fileName, verbosity)
46
47 def getFileFormats():
48 return ["map"]
49 getFileFormats = staticmethod(getFileFormats)
50
51 def skipFirstLines(self):
52 return
53
54 def parseLine(self, line):
55 m = self._lineParseRe.search(line)
56
57 if m == None:
58 sys.exit("\nLine %d '%s' does not have a map format" % (self.currentLineNb, line))
59
60 transcript = Transcript()
61 transcript.setChromosome(m.group("chrName"))
62 transcript.setStart(min(int(m.group("sStart")), int(m.group("sEnd"))))
63 transcript.setEnd(max(int(m.group("sStart")), int(m.group("sEnd"))))
64 transcript.setName(m.group("seqName"))
65 transcript.setDirection(1)
66
67 return transcript