Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/ShrimpParser.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 SMART.Java.Python.structure.Mapping import Mapping
33 from commons.core.parsing.MapperParser import MapperParser
34
35
36 class ShrimpParser(MapperParser):
37 """A class that parses the output of Shrimp"""
38
39 def __init__(self, fileName, verbosity = 0):
40 super(ShrimpParser, self).__init__(fileName, verbosity)
41
42
43 def __del__(self):
44 super(ShrimpParser, self).__del__()
45
46
47 def getFileFormats():
48 return ["shrimp"]
49 getFileFormats = staticmethod(getFileFormats)
50
51
52 def skipFirstLines(self):
53 self.handle.readline()
54 self.currentLineNb += 1
55
56
57 def parseLine(self, line):
58 m = re.search(r"^\s*>([^\t]+)\t+(\S+)\s+([+-])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*$", line)
59 if m == None:
60 sys.exit("\nLine %d '%s' does not have a Shrimp format" % (self.currentLineNb, line))
61
62 mapping = Mapping()
63
64 mapping.queryInterval.setName(m.group(1))
65 mapping.queryInterval.setStart(min(int(m.group(6)), int(m.group(7))))
66 mapping.queryInterval.setEnd(max(int(m.group(6)), int(m.group(7))))
67
68 mapping.targetInterval.setChromosome(m.group(2))
69 mapping.targetInterval.setStart(min(int(m.group(4)), int(m.group(5))))
70 mapping.targetInterval.setEnd(max(int(m.group(4)), int(m.group(5))))
71
72 mapping.setSize(int(m.group(8)))
73 mapping.setDirection(m.group(3))
74
75 editString = m.group(10)
76 nbMismatches = 0
77 nbGaps = 0
78 while editString != "":
79 m = re.search(r"^(\d+)(\D.*)$", editString)
80 if m != None:
81 editString = m.group(2)
82 else:
83 m = re.search(r"^(\d+)$", editString)
84 if m != None:
85 editString = ""
86 else:
87 m = re.search(r"^([A-Z])(.*)$", editString)
88 if m != None:
89 nbMismatches += 1
90 editString = m.group(2)
91 else:
92 m = re.search(r"^\((\w+)\)(.*)$", editString)
93 if m != None:
94 nbGaps += len(m.group(1))
95 editString = m.group(2)
96 else:
97 m = re.search(r"^-(.*)$", editString)
98 if m != None:
99 nbGaps += 1
100 editString = m.group(1)
101 else:
102 sys.exit("Cannot understand edit string %s from line %s" % (editString, line))
103
104 mapping.setNbMismatches(nbMismatches)
105 mapping.setNbGaps(nbGaps)
106
107 return mapping