Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/Soap2Parser.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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 SMART.Java.Python.structure.Mapping import Mapping | |
33 from SMART.Java.Python.structure.SubMapping import SubMapping | |
34 from commons.core.parsing.MapperParser import MapperParser | |
35 | |
36 | |
37 def mappingToSubMapping(mapping): | |
38 subMapping = SubMapping() | |
39 subMapping.targetInterval.copy(mapping.targetInterval) | |
40 subMapping.queryInterval.copy(mapping.queryInterval) | |
41 subMapping.setDirection(mapping.getDirection()) | |
42 subMapping.size = mapping.size | |
43 subMapping.tags = mapping.tags | |
44 return subMapping | |
45 | |
46 | |
47 | |
48 class Soap2Parser(MapperParser): | |
49 """A class that parses the output of SOAP2""" | |
50 | |
51 def __init__(self, fileName, verbosity = 0): | |
52 super(Soap2Parser, self).__init__(fileName, verbosity) | |
53 | |
54 | |
55 def __del__(self): | |
56 super(Soap2Parser, self).__del__() | |
57 | |
58 | |
59 def getFileFormats(): | |
60 return ["soap2"] | |
61 getFileFormats = staticmethod(getFileFormats) | |
62 | |
63 | |
64 def skipFirstLines(self): | |
65 pass | |
66 | |
67 | |
68 def getIterator(self): | |
69 self.reset() | |
70 currentName = None | |
71 currentMappings = [] | |
72 for line in self.handle: | |
73 mapping = self.parseLine(line) | |
74 name = mapping.queryInterval.name | |
75 if name == currentName: | |
76 if mapping.getTagValue("end") == "a": | |
77 currentMappings.append(mapping) | |
78 else: | |
79 otherEndMapping = currentMappings.pop(0) | |
80 | |
81 newMapping = Mapping() | |
82 subMappingA = mappingToSubMapping(otherEndMapping) | |
83 subMappingB = mappingToSubMapping(mapping) | |
84 subMappingB.queryInterval.setDirection(subMappingA.queryInterval.getDirection()) | |
85 | |
86 newMapping.addSubMapping(subMappingA) | |
87 newMapping.addSubMapping(subMappingB) | |
88 | |
89 newMapping.tags = otherEndMapping.tags | |
90 newMapping.setSize(otherEndMapping.size + mapping.size) | |
91 newMapping.setNbMismatches(otherEndMapping.getTagValue("nbMismatches") + mapping.getTagValue("nbMismatches")) | |
92 print otherEndMapping.getTagValue("nbMismatches") | |
93 print mapping.getTagValue("nbMismatches") | |
94 print newMapping.getTagValue("nbMismatches") | |
95 sys.exit() | |
96 newMapping.setTagValue("qualityString", otherEndMapping.getTagValue("qualityString") + mapping.getTagValue("qualityString")) | |
97 newMapping.setTagValue("occurrence", "%d" % (newMapping.getTagValue("nbOccurrences") - len(currentMappings))) | |
98 newMapping.setTagValue("ID", "%s-%s" % (name, newMapping.getTagValue("occurrence"))) | |
99 del newMapping.tags["end"] | |
100 yield newMapping | |
101 else: | |
102 currentName = mapping.queryInterval.name | |
103 for currentMapping in currentMappings: | |
104 yield currentMapping | |
105 currentMappings = [mapping] | |
106 self.currentLineNb += 1 | |
107 | |
108 | |
109 def parseLine(self, line): | |
110 m = re.search(r"^\s*(\S+)\s+(\w+)\s+(\S+)\s+(\d+)\s+([ab])\s+(\d+)\s+([+-])\s+(\w+)\s+(\d+)\s+(\d+)\s+", line) | |
111 if m == None: | |
112 sys.exit("\nLine %d '%s' does not have a SOAP2 format" % (self.currentLineNb, line)) | |
113 | |
114 name = m.group(1) | |
115 read = m.group(2) | |
116 qualityString = m.group(3) | |
117 nbOccurrences = int(m.group(4)) | |
118 end = m.group(5) | |
119 size = int(m.group(6)) | |
120 direction = m.group(7) | |
121 chromosome = m.group(8) | |
122 genomeStart = int(m.group(9)) | |
123 nbMismatches = int(m.group(10)) | |
124 | |
125 mapping = Mapping() | |
126 if name.endswith("/1") or name.endswith("/2"): | |
127 name = name[:-2] | |
128 | |
129 mapping.queryInterval.name = name | |
130 mapping.queryInterval.setDirection(direction) | |
131 mapping.queryInterval.setStart(1) | |
132 mapping.queryInterval.setEnd(size) | |
133 | |
134 mapping.targetInterval.setChromosome(chromosome) | |
135 mapping.targetInterval.setStart(genomeStart) | |
136 mapping.targetInterval.setSize(size) | |
137 | |
138 mapping.setDirection(direction) | |
139 mapping.setSize(size) | |
140 | |
141 mapping.setNbMismatches(nbMismatches) | |
142 mapping.setNbGaps(0) | |
143 mapping.setTagValue("qualityString", qualityString) | |
144 mapping.setTagValue("nbOccurrences", nbOccurrences) | |
145 mapping.setTagValue("end", end) | |
146 | |
147 return mapping | |
148 |