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comparison commons/core/parsing/MaqParser.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 #
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
35
36 class MaqParser(MapperParser):
37 """A class that parses the output of Maq"""
38
39 def __init__(self, fileName, verbosity = 0):
40 super(MaqParser, self).__init__(fileName, verbosity)
41
42
43 def __del__(self):
44 super(MaqParser, self).__del__()
45
46
47 def getFileFormats():
48 return ["maq"]
49 getFileFormats = staticmethod(getFileFormats)
50
51
52 def skipFirstLines(self):
53 pass
54
55
56 def parseLine(self, line):
57 m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\d+)\s+([+-])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s*$", line)
58 if m == None:
59 sys.exit("\nLine %d '%s' does not have a MAQ format" % (self.currentLineNb, line))
60
61 mapping = Mapping()
62
63 mapping.targetInterval.setStart(int(m.group(3)))
64 mapping.targetInterval.setSize(int(m.group(14)))
65 mapping.targetInterval.setChromosome(m.group(2))
66
67 mapping.queryInterval.setStart(1)
68 mapping.queryInterval.setSize(int(m.group(14)))
69 mapping.queryInterval.setName(m.group(1))
70
71 mapping.setDirection(m.group(4))
72 mapping.setSize(int(m.group(14)))
73 mapping.setNbMismatches(int(m.group(10)))
74 mapping.setRank(1)
75 mapping.setNbOccurrences(int(m.group(12)) + int(m.group(13)))
76
77 return mapping