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comparison smart_toolShed/commons/core/parsing/SamParser.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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 from SMART.Java.Python.structure.Interval import Interval
36
37 class SamParser(MapperParser):
38 """A class that parses SAM format (as given by BWA)"""
39
40 def __init__(self, fileName, verbosity = 0):
41 super(SamParser, self).__init__(fileName, verbosity)
42
43
44 def __del__(self):
45 super(SamParser, self).__del__()
46
47
48 def getFileFormats():
49 return ["sam"]
50 getFileFormats = staticmethod(getFileFormats)
51
52
53 def skipFirstLines(self):
54 pass
55
56
57 def getInfos(self):
58 self.chromosomes = set()
59 self.nbMappings = 0
60 self.size = 0
61 self.reset()
62 if self.verbosity >= 10:
63 print "Getting information on SAM file"
64 self.reset()
65 for line in self.handle:
66 line = line.strip()
67 if line == "" or line[0] == "@":
68 continue
69 parts = line.split("\t")
70 chromosome = parts[2]
71 if chromosome != "*":
72 self.chromosomes.add(chromosome)
73 self.nbMappings += 1
74 self.size += len(parts[8])
75 if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
76 sys.stdout.write(" %d mappings read\r" % (self.nbMappings))
77 sys.stdout.flush()
78 self.reset()
79 if self.verbosity >= 10:
80 print " %d mappings read" % (self.nbMappings)
81 print "Done."
82
83
84 def parseLine(self, line):
85
86 line = line.strip()
87 if line[0] == "@":
88 return
89
90 fields = line.split("\t")
91 if len(fields) < 11:
92 raise Exception("Line %d '%s' does not look like a SAM line (number of fields is %d instead of 11)" % (self.currentLineNb, line, len(fields)))
93
94 name = fields[0]
95 flag = int(fields[1])
96
97 if (flag & 0x4) == 0x4:
98 return None
99
100 direction = 1 if (flag & 0x10) == 0x0 else -1
101 chromosome = fields[2]
102 genomeStart = int(fields[3])
103 quality = fields[4]
104 cigar = fields[5]
105 mate = fields[6]
106 mateGenomeStart = fields[7]
107 gapSize = fields[8]
108 sequence = fields[9]
109 quality = fields[10]
110 tags = fields[11:]
111
112 if mateGenomeStart != "*":
113 mateGenomeStart = int(mateGenomeStart)
114
115 mapping = Mapping()
116 nbOccurrences = 1
117 nbMismatches = 0
118 nbMatches = 0
119 nbGaps = 0
120 subMapping = None
121 queryOffset = 0
122 targetOffset = 0
123 currentNumber = 0
124 readStart = None
125
126 for tag in tags:
127 key = tag[:2]
128 if key == "X0":
129 nbOccurrences = int(tag[5:])
130 elif key == "X1":
131 nbOccurrences += int(tag[5:])
132 elif key == "XM":
133 nbMismatches = int(tag[5:])
134 mapping.setTagValue("nbOccurrences", nbOccurrences)
135 mapping.setTagValue("quality", int(fields[4]))
136
137 for char in cigar:
138 m = re.match(r"[0-9]", char)
139 if m != None:
140 currentNumber = currentNumber * 10 + (ord(char) - ord("0"))
141 continue
142 # match
143 m = re.match(r"[M]", char)
144 if m != None:
145 if readStart == None:
146 readStart = queryOffset
147 if subMapping == None:
148 subMapping = SubMapping()
149 subMapping.setSize(currentNumber)
150 subMapping.setDirection(direction)
151 subMapping.queryInterval.setName(name)
152 subMapping.queryInterval.setStart(queryOffset)
153 subMapping.queryInterval.setDirection(direction)
154 subMapping.targetInterval.setChromosome(chromosome)
155 subMapping.targetInterval.setStart(genomeStart + targetOffset)
156 subMapping.targetInterval.setDirection(1)
157 nbMatches += currentNumber
158 targetOffset += currentNumber
159 queryOffset += currentNumber
160 currentNumber = 0
161 continue
162 # insertion on the read
163 m = re.match(r"[I]", char)
164 if m != None:
165 nbGaps += 1
166 queryOffset += currentNumber
167 currentNumber = 0
168 continue
169 # insertion on the genome
170 m = re.match(r"[D]", char)
171 if m != None:
172 if subMapping != None:
173 subMapping.queryInterval.setEnd(queryOffset - 1)
174 subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
175 mapping.addSubMapping(subMapping)
176 subMapping = None
177 nbGaps += 1
178 targetOffset += currentNumber
179 currentNumber = 0
180 continue
181 # intron
182 m = re.match(r"[N]", char)
183 if m != None:
184 if subMapping != None:
185 subMapping.queryInterval.setEnd(queryOffset - 1)
186 subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
187 mapping.addSubMapping(subMapping)
188 subMapping = None
189 targetOffset += currentNumber
190 currentNumber = 0
191 continue
192 # soft clipping (substitution)
193 m = re.match(r"[S]", char)
194 if m != None:
195 nbMismatches += currentNumber
196 targetOffset += currentNumber
197 queryOffset += currentNumber
198 currentNumber = 0
199 continue
200 # hard clipping
201 m = re.match(r"[H]", char)
202 if m != None:
203 targetOffset += currentNumber
204 queryOffset += currentNumber
205 currentNumber = 0
206 continue
207 # padding
208 m = re.match(r"[P]", char)
209 if m != None:
210 continue
211 raise Exception("Do not understand paramer '%s' in line %s" % (char, line))
212
213 if subMapping != None:
214 subMapping.queryInterval.setEnd(queryOffset - 1)
215 subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
216 mapping.addSubMapping(subMapping)
217
218 mapping.queryInterval.setStart(readStart)
219 mapping.queryInterval.setEnd(queryOffset - 1)
220 mapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
221 mapping.setNbMismatches(nbMismatches)
222 mapping.setNbGaps(nbGaps)
223
224 mapping.queryInterval.setName(name)
225 mapping.queryInterval.setDirection(direction)
226 mapping.targetInterval.setChromosome(chromosome)
227 mapping.targetInterval.setStart(genomeStart)
228 mapping.targetInterval.setDirection(direction)
229 mapping.setSize(len(sequence))
230 mapping.setDirection(direction)
231
232 return mapping
233
234