Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/CoordsParser.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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 commons.core.parsing.MapperParser import MapperParser
34 from SMART.Java.Python.structure.SubMapping import SubMapping
35 from SMART.Java.Python.misc import Utils
36
37 class CoordsParser(MapperParser):
38 """A class that parses the .coords output of Nucmer"""
39
40 def __init__(self, fileName, verbosity = 0):
41 self._lineParseRe = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+\|\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
42 self._lineParseRe2 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
43 self._lineParseRe3 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+\|\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
44 self._lineParseRe4 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
45 self.lineType = 1
46 MapperParser.__init__(self, fileName, verbosity)
47
48 def getFileFormats():
49 return ["coords"]
50 getFileFormats = staticmethod(getFileFormats)
51
52 def skipFirstLines(self):
53 while True:
54 line = self.handle.readline()
55 self.currentLineNb += 1
56 if line == "":
57 break
58 if "=====" in line:
59 break
60 if "[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]" in line:
61 self.lineType = 2
62 break
63 if "[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] [% SIM] [% STP] | [FRM] [TAGS]" in line:
64 self.lineType = 3
65
66 if "[% IDY]\t[% SIM]\t[% STP]" in line and "[LEN Q]"in line:
67 self.lineType = 4
68 break
69
70 def parseLine(self, line):
71
72 if self.lineType == 1 :
73 m = self._lineParseRe.search(line)
74 elif self.lineType == 2:
75 m = self._lineParseRe2.search(line)
76 elif self.lineType == 3:
77 m = self._lineParseRe3.search(line)
78 elif self.lineType == 4:
79 m = self._lineParseRe4.search(line)
80 if m == None:
81 sys.exit("\nLine %d '%s' does not have a NucMer format" % (self.currentLineNb, line))
82
83 mapping = Mapping()
84
85 subMapping = SubMapping()
86 subMapping.queryInterval.setName(m.group("qName"))
87 subMapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd"))))
88 subMapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd"))))
89 subMapping.queryInterval.setSize(int(m.group("qLength")))
90 subMapping.queryInterval.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
91
92 subMapping.targetInterval.setChromosome(m.group("tName"))
93 subMapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd"))))
94 subMapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd"))))
95 subMapping.targetInterval.setSize(int(m.group("tLength")))
96 subMapping.targetInterval.setDirection(int(m.group("tEnd")) - int(m.group("tStart")))
97
98 subMapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
99 subMapping.setSize(min(int(m.group("qLength")), int(m.group("tLength"))))
100 subMapping.setIdentity(float(m.group("identity")))
101
102 mapping.addSubMapping(subMapping)
103 mapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd"))))
104 mapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd"))))
105 mapping.targetInterval.setSize(int(m.group("tLength")))
106 mapping.targetInterval.setChromosome(m.group("tName"))
107
108 mapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd"))))
109 mapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd"))))
110 mapping.queryInterval.setSize(int(m.group("qLength")))
111 mapping.queryInterval.setName(m.group("qName"))
112 mapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
113 mapping.setSize(min(int(m.group("qLength")), int(m.group("tLength"))))
114 mapping.setIdentity(float(m.group("identity")))
115 mapping.setTagValue("feature", "match")
116 mapping.setTagValue("Target", "%s %d %d" % (m.group("qName"), int(m.group("qStart")), int(m.group("qEnd"))))
117
118 if self.lineType ==2 or self.lineType ==4:
119 mapping.setTagValue("target_pident", float(m.group("identity")))
120 mapping.setTagValue("target_pcover", float(m.group("qcov")))
121 mapping.setTagValue("target_length", int(m.group("qlen")))
122
123
124 # Specific to Mark Work. Commented lines because of possible slowdown.
125 # for line in self.handle:
126 # string1 = line.strip()
127 # self.currentLineNb += 1
128 # break
129 # for line in self.handle:
130 # string2 = line.strip()
131 # self.currentLineNb += 1
132 # break
133 # print(len(string1),len(string2))
134 # mapping.setNbMismatches(Utils.getHammingDistance(string1, string2))
135 mapping.setNbGaps(0)
136
137 return mapping