Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/BlastParser.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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 commons.core.parsing.MapperParser import MapperParser
33 from SMART.Java.Python.structure.Interval import Interval
34 from SMART.Java.Python.structure.SubMapping import SubMapping
35 from SMART.Java.Python.structure.Mapping import Mapping
36
37
38 class BlastParser(MapperParser):
39 """A class that parses the output of Blast (-m 8 format)"""
40
41 def __init__(self, fileName, verbosity = 0):
42 super(BlastParser, self).__init__(fileName, verbosity)
43
44
45 def __del__(self):
46 super(BlastParser, self).__del__()
47
48
49 def getFileFormats():
50 return ["blast"]
51 getFileFormats = staticmethod(getFileFormats)
52
53
54 def skipFirstLines(self):
55 pass
56
57
58 def parseLine(self, line):
59 m = re.search(r"^(\S+)\s+(\S+)\s+(\d+\.?\d*)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+([-+]?\d+\.?\d*[eE]?[-+]?\d*)\s+(\d+\.?\d*)\s*$", line)
60 if m == None:
61 sys.exit("\nLine %d '%s' does not have an Blast format" % (self.currentLineNb, line))
62
63 mapping = Mapping()
64
65 queryInterval = Interval()
66 queryInterval.setName(m.group(1))
67 queryInterval.setStart(min(int(m.group(7)), int(m.group(8))))
68 queryInterval.setEnd(max(int(m.group(7)), int(m.group(8))))
69
70 targetInterval = Interval()
71 targetInterval.setChromosome(m.group(2))
72 targetInterval.setStart(min(int(m.group(9)), int(m.group(10))))
73 targetInterval.setEnd(max(int(m.group(9)), int(m.group(10))))
74
75 subMapping = SubMapping()
76 subMapping.setQueryInterval(queryInterval)
77 subMapping.setTargetInterval(targetInterval)
78
79 mapping.addSubMapping(subMapping)
80
81 mapping.setIdentity(round(float(m.group(3))))
82 mapping.setSize(int(m.group(4)))
83 mapping.setNbMismatches(int(m.group(5)))
84 mapping.setNbGaps(int(m.group(6)))
85 mapping.setDirection((int(m.group(8)) - int(m.group(7))) * (int(m.group(10)) - int(m.group(9))))
86 mapping.setEvalue(float(m.group(11)))
87
88 return mapping