annotate commons/core/parsing/PslParser.py @ 57:36eaa579fdb6

Uploaded
author m-zytnicki
date Fri, 07 Feb 2014 08:29:48 -0500
parents 769e306b7933
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 # Copyright INRA-URGI 2009-2010
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 # This software is governed by the CeCILL license under French law and
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 # abiding by the rules of distribution of free software. You can use,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 # modify and/ or redistribute the software under the terms of the CeCILL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 # license as circulated by CEA, CNRS and INRIA at the following URL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 # "http://www.cecill.info".
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 # As a counterpart to the access to the source code and rights to copy,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 # modify and redistribute granted by the license, users are provided only
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 # with a limited warranty and the software's author, the holder of the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 # economic rights, and the successive licensors have only limited
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 # liability.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 # In this respect, the user's attention is drawn to the risks associated
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 # with loading, using, modifying and/or developing or reproducing the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 # software by the user in light of its specific status of free software,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 # that may mean that it is complicated to manipulate, and that also
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 # therefore means that it is reserved for developers and experienced
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 # professionals having in-depth computer knowledge. Users are therefore
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 # encouraged to load and test the software's suitability as regards their
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 # requirements in conditions enabling the security of their systems and/or
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 # data to be ensured and, more generally, to use and operate it in the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 # same conditions as regards security.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 # The fact that you are presently reading this means that you have had
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 # knowledge of the CeCILL license and that you accept its terms.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 import re
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 import sys
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 from commons.core.parsing.MapperParser import MapperParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 from SMART.Java.Python.structure.Mapping import Mapping
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 from SMART.Java.Python.structure.SubMapping import SubMapping
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 from SMART.Java.Python.structure.Interval import Interval
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 class PslParser(MapperParser):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 """A class that parses the output of PSL format (of SSAHA and BLAT)"""
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 def __init__(self, fileName, verbosity = 0):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 super(PslParser, self).__init__(fileName, verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 def __del__(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 super(PslParser, self).__del__()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 def getFileFormats():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 return ["psl"]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 getFileFormats = staticmethod(getFileFormats)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 def getInfos(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 self.chromosomes = set()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 self.nbMappings = 0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 self.size = 0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 self.reset()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 progress = UnlimitedProgress(100000, "Getting info on PSL file, # mappings read:", self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 for line in self.handle:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 progress.inc()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 line = line.strip()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 continue
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 parts = line.split("\t")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 chromosome = parts[13]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 self.chromosomes.add(chromosome)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 self.nbMappings += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 self.size += len(parts[0])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 self.reset()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 progress.done()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 def skipFirstLines(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 while "------" not in self.handle.readline():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 self.currentLineNb += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 pass
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 def _computeStarts(self,seqSize,blockSize,start,targetStrand):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 if targetStrand == "+":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81 pass
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 start = seqSize-blockSize-start
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84 return start
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 def parseLine(self, line):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 if m == None:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91 raise Exception("\nLine %d '%s' does not have a PSL format" % (self.currentLineNb, line))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
92
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
93 mapping = Mapping()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
94
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
95 queryStrand = m.group(7)[0]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
96
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
97 if len(m.group(7)) == 1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
98 targetStrand = "+"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
99 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
100 targetStrand = m.group(7)[1]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
101
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
102
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
103 for i in range(0, int(m.group(16))):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
104 size = int(m.group(17).split(",")[i])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
105 queryStart = int(m.group(18).split(",")[i])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
106 targetStart = int(m.group(19).split(",")[i])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
107 querySize = int(m.group(9))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
108 targetSize = int(m.group(13))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
109
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
110 subMapping = SubMapping()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
111 subMapping.setSize(size)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
112 subMapping.setDirection(m.group(7)[0])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
113
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
114 queryInterval = Interval()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
115 targetInterval = Interval()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
116
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
117 queryInterval.setName(m.group(8))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
118 queryStart = self._computeStarts(querySize,size,queryStart,targetStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
119 queryInterval.setStart(queryStart + 1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
120 queryInterval.setEnd(queryStart + size)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
121 queryInterval.setDirection(queryStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
122
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
123 targetInterval.setChromosome(m.group(12))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
124 targetStart = self._computeStarts(targetSize,size,targetStart,targetStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
125 targetInterval.setStart(targetStart + 1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
126 targetInterval.setEnd(targetStart + size)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
127 targetInterval.setDirection(targetStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
128
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
129 subMapping.setQueryInterval(queryInterval)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
130 subMapping.setTargetInterval(targetInterval)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
131 mapping.addSubMapping(subMapping)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
132
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
133 mapping.setSize(int(m.group(2)) + int(m.group(3)) + int(m.group(4)))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
134 mapping.setNbMismatches(int(m.group(3)) + int(m.group(4)))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
135 mapping.setNbGaps(int(m.group(5)))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
136 mapping.setDirection(queryStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
137
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
138 queryInterval = Interval()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
139 targetInterval = Interval()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
140
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
141 queryInterval.setName(m.group(8))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
142 queryInterval.setStart(min(int(m.group(10)), int(m.group(11))))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
143 queryInterval.setEnd( max(int(m.group(10)), int(m.group(11))))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
144 queryInterval.setDirection(queryStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
145
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
146 targetInterval.setChromosome(m.group(12))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
147 targetInterval.setStart(min(int(m.group(14))+1, int(m.group(15))))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
148 targetInterval.setEnd( max(int(m.group(14))+1, int(m.group(15))))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
149 targetInterval.setDirection(targetStrand)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
150
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
151 mapping.setQueryInterval(queryInterval)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
152 mapping.setTargetInterval(targetInterval)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
153
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
154 return mapping
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
155