Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/PslParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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 from SMART.Java.Python.structure.Interval import Interval | |
36 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress | |
37 | |
38 class PslParser(MapperParser): | |
39 """A class that parses the output of PSL format (of SSAHA and BLAT)""" | |
40 | |
41 def __init__(self, fileName, verbosity = 0): | |
42 super(PslParser, self).__init__(fileName, verbosity) | |
43 | |
44 | |
45 def __del__(self): | |
46 super(PslParser, self).__del__() | |
47 | |
48 | |
49 def getFileFormats(): | |
50 return ["psl"] | |
51 getFileFormats = staticmethod(getFileFormats) | |
52 | |
53 | |
54 def getInfos(self): | |
55 self.chromosomes = set() | |
56 self.nbMappings = 0 | |
57 self.size = 0 | |
58 self.reset() | |
59 progress = UnlimitedProgress(100000, "Getting info on PSL file, # mappings read:", self.verbosity) | |
60 for line in self.handle: | |
61 progress.inc() | |
62 line = line.strip() | |
63 if line == "": | |
64 continue | |
65 parts = line.split("\t") | |
66 chromosome = parts[13] | |
67 self.chromosomes.add(chromosome) | |
68 self.nbMappings += 1 | |
69 self.size += len(parts[0]) | |
70 self.reset() | |
71 progress.done() | |
72 | |
73 | |
74 def skipFirstLines(self): | |
75 while "------" not in self.handle.readline(): | |
76 self.currentLineNb += 1 | |
77 pass | |
78 | |
79 def _computeStarts(self,seqSize,blockSize,start,targetStrand): | |
80 if targetStrand == "+": | |
81 pass | |
82 else: | |
83 start = seqSize-blockSize-start | |
84 return start | |
85 | |
86 | |
87 | |
88 def parseLine(self, line): | |
89 m = re.search(r"^\s*(psl:\s+)?(\d+)\s+(\d+)\s+(\d+)\s+\d+\s+\d+\s+(\d+)\s+\d+\s+(\d+)\s+([+-]{1,2})\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s*$", line) | |
90 if m == None: | |
91 raise Exception("\nLine %d '%s' does not have a PSL format" % (self.currentLineNb, line)) | |
92 | |
93 mapping = Mapping() | |
94 | |
95 queryStrand = m.group(7)[0] | |
96 | |
97 if len(m.group(7)) == 1: | |
98 targetStrand = "+" | |
99 else: | |
100 targetStrand = m.group(7)[1] | |
101 | |
102 | |
103 for i in range(0, int(m.group(16))): | |
104 size = int(m.group(17).split(",")[i]) | |
105 queryStart = int(m.group(18).split(",")[i]) | |
106 targetStart = int(m.group(19).split(",")[i]) | |
107 querySize = int(m.group(9)) | |
108 targetSize = int(m.group(13)) | |
109 | |
110 subMapping = SubMapping() | |
111 subMapping.setSize(size) | |
112 subMapping.setDirection(m.group(7)[0]) | |
113 | |
114 queryInterval = Interval() | |
115 targetInterval = Interval() | |
116 | |
117 queryInterval.setName(m.group(8)) | |
118 queryStart = self._computeStarts(querySize,size,queryStart,targetStrand) | |
119 queryInterval.setStart(queryStart + 1) | |
120 queryInterval.setEnd(queryStart + size) | |
121 queryInterval.setDirection(queryStrand) | |
122 | |
123 targetInterval.setChromosome(m.group(12)) | |
124 targetStart = self._computeStarts(targetSize,size,targetStart,targetStrand) | |
125 targetInterval.setStart(targetStart + 1) | |
126 targetInterval.setEnd(targetStart + size) | |
127 targetInterval.setDirection(targetStrand) | |
128 | |
129 subMapping.setQueryInterval(queryInterval) | |
130 subMapping.setTargetInterval(targetInterval) | |
131 mapping.addSubMapping(subMapping) | |
132 | |
133 mapping.setSize(int(m.group(2)) + int(m.group(3)) + int(m.group(4))) | |
134 mapping.setNbMismatches(int(m.group(3)) + int(m.group(4))) | |
135 mapping.setNbGaps(int(m.group(5))) | |
136 mapping.setDirection(queryStrand) | |
137 | |
138 queryInterval = Interval() | |
139 targetInterval = Interval() | |
140 | |
141 queryInterval.setName(m.group(8)) | |
142 queryInterval.setStart(min(int(m.group(10)), int(m.group(11)))) | |
143 queryInterval.setEnd( max(int(m.group(10)), int(m.group(11)))) | |
144 queryInterval.setDirection(queryStrand) | |
145 | |
146 targetInterval.setChromosome(m.group(12)) | |
147 targetInterval.setStart(min(int(m.group(14))+1, int(m.group(15)))) | |
148 targetInterval.setEnd( max(int(m.group(14))+1, int(m.group(15)))) | |
149 targetInterval.setDirection(targetStrand) | |
150 | |
151 mapping.setQueryInterval(queryInterval) | |
152 mapping.setTargetInterval(targetInterval) | |
153 | |
154 return mapping | |
155 |