Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/NucmerParser.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.SubMapping import SubMapping
33 from SMART.Java.Python.structure.Mapping import Mapping
34 from SMART.Java.Python.structure.Interval import Interval
35 from commons.core.parsing.MapperParser import MapperParser
36
37
38 class NucmerParser(MapperParser):
39 """A class that parses the output of Nucmer"""
40
41 def __init__(self, fileName, verbosity = 0):
42 super(NucmerParser, self).__init__(fileName, verbosity)
43
44
45 def __del__(self):
46 super(NucmerParser, self).__del__()
47
48
49 def getFileFormats():
50 return ["nucmer"]
51 getFileFormats = staticmethod(getFileFormats)
52
53
54 def skipFirstLines(self):
55 pass
56
57
58 def parseLine(self, line):
59 if not line:
60 return None
61 if line[0] == ">":
62 self.currentChromosome = line[1:].split()[0]
63 return None
64 splittedLine = line.strip().split()
65 if len(splittedLine) != 8:
66 raise Exception("Line %d '%s' does not have a NucMer format" % (self.currentLineNb, line))
67
68 subMapping = SubMapping()
69
70 subMapping.targetInterval.setChromosome(self.currentChromosome)
71 subMapping.targetInterval.setName(self.currentChromosome)
72 subMapping.targetInterval.setStart(min(int(splittedLine[0]), int(splittedLine[1])))
73 subMapping.targetInterval.setEnd(max(int(splittedLine[0]), int(splittedLine[1])))
74 subMapping.targetInterval.setDirection(splittedLine[6])
75
76 subMapping.queryInterval.setChromosome(splittedLine[7])
77 subMapping.queryInterval.setName(splittedLine[7])
78 subMapping.queryInterval.setStart(1)
79 subMapping.queryInterval.setEnd(int(splittedLine[3]))
80 subMapping.queryInterval.setDirection("+")
81
82 mapping = Mapping()
83 mapping.addSubMapping(subMapping)
84 mapping.setDirection(splittedLine[6])
85 mapping.setIdentity(float(splittedLine[5]))
86 mapping.setSize(int(splittedLine[3]))
87
88 return mapping