Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/ExoParser.py @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
parents | 769e306b7933 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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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.Mapping import Mapping | |
34 from SMART.Java.Python.structure.SubMapping import SubMapping | |
35 | |
36 class ExoParser(MapperParser): | |
37 """A class that parses the output of Exonerate - roll your own format""" | |
38 | |
39 def __init__(self, fileName, verbosity = 0): | |
40 super(ExoParser, self).__init__(fileName, verbosity) | |
41 | |
42 | |
43 def __del__(self): | |
44 super(ExoParser, self).__del__() | |
45 | |
46 | |
47 def getFileFormats(): | |
48 return ["exo", "exonerate"] | |
49 getFileFormats = staticmethod(getFileFormats) | |
50 | |
51 | |
52 def skipFirstLines(self): | |
53 while "Hostname" not in self.handle.readline(): | |
54 self.currentLineNb += 1 | |
55 pass | |
56 | |
57 | |
58 def parseLine(self, line): | |
59 | |
60 if line == "-- completed exonerate analysis\n": | |
61 return None | |
62 | |
63 m = re.search(r"^\s*(\S+)\s+(\d+)\s+(\d+)\s+[+-]\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s+(\d+)\s+(\S.*)$", line) | |
64 if m == None: | |
65 sys.exit("\nLine %d '%s' does not have a RYO format" % (self.currentLineNb, line)) | |
66 | |
67 mapping = Mapping() | |
68 name = m.group(1) | |
69 queryStart = min(int(m.group(2)), int(m.group(3))) | |
70 queryEnd = max(int(m.group(2)), int(m.group(3)))-1 | |
71 chromosome = m.group(4) | |
72 targetStart = min(int(m.group(5)), int(m.group(6))) | |
73 targetEnd = max(int(m.group(5)), int(m.group(6)))-1 | |
74 direction = m.group(7) | |
75 nbMismatches = int(m.group(8)) | |
76 rest = m.group(9).strip() | |
77 | |
78 nbGaps = 0 | |
79 queryOffset = 0 | |
80 targetOffset = 0 | |
81 | |
82 subMapping = None | |
83 m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest) | |
84 while m != None: | |
85 queryDistance = int(m.group(2)) | |
86 targetDistance = int(m.group(3)) | |
87 if m.group(1) == "M": | |
88 if subMapping == None: | |
89 subMapping = SubMapping() | |
90 | |
91 subMapping.setSize(queryDistance) | |
92 subMapping.setDirection(direction) | |
93 | |
94 subMapping.queryInterval.setName(name) | |
95 subMapping.queryInterval.setStart(queryStart + queryOffset) | |
96 subMapping.queryInterval.setDirection(direction) | |
97 | |
98 subMapping.targetInterval.setChromosome(chromosome) | |
99 subMapping.targetInterval.setStart(targetStart + targetOffset) | |
100 subMapping.targetInterval.setDirection(1) | |
101 | |
102 elif m.group(1) == "G": | |
103 nbGaps += max(queryDistance, targetDistance) | |
104 | |
105 elif m.group(1) == "I" or m.group(1) == "5" or m.group(1) == "3": | |
106 if subMapping != None: | |
107 subMapping.queryInterval.setEnd(queryStart + queryOffset - 1) | |
108 subMapping.targetInterval.setEnd(targetStart + targetOffset - 1) | |
109 mapping.addSubMapping(subMapping) | |
110 subMapping = None | |
111 else: | |
112 sys.exit("Cannot understand sign '%s' in line %s" % (m.group(1), line)) | |
113 | |
114 queryOffset += queryDistance | |
115 targetOffset += targetDistance | |
116 rest = rest[m.end():].strip() | |
117 m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest) | |
118 | |
119 if subMapping != None: | |
120 subMapping.queryInterval.setEnd(queryStart + queryOffset - 1) | |
121 subMapping.targetInterval.setEnd(targetStart + targetOffset - 1) | |
122 mapping.addSubMapping(subMapping) | |
123 | |
124 mapping.setNbMismatches(nbMismatches) | |
125 mapping.setNbGaps(nbGaps) | |
126 mapping.setDirection(direction) | |
127 | |
128 mapping.queryInterval.setName(name) | |
129 mapping.queryInterval.setStart(queryStart) | |
130 mapping.queryInterval.setEnd(queryEnd) | |
131 | |
132 mapping.targetInterval.setChromosome(chromosome) | |
133 mapping.targetInterval.setStart(targetStart) | |
134 mapping.targetInterval.setEnd(targetEnd) | |
135 | |
136 return mapping | |
137 |