|
6
|
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 from SMART.Java.Python.misc import Utils
|
|
|
36 from SMART.Java.Python.misc.Utils import getHammingDistance
|
|
|
37
|
|
|
38
|
|
|
39 class AxtParser(MapperParser):
|
|
|
40 """A class that parses AXT (as given by Mosaik)"""
|
|
|
41
|
|
|
42 def __init__(self, fileName, verbosity = 0):
|
|
|
43 super(AxtParser, self).__init__(fileName, verbosity)
|
|
|
44 self.queryLine = None
|
|
|
45 self.subjectLine = None
|
|
|
46
|
|
|
47 def __del__(self):
|
|
|
48 super(AxtParser, self).__del__()
|
|
|
49
|
|
|
50
|
|
|
51 def getFileFormats():
|
|
|
52 return ["axt"]
|
|
|
53 getFileFormats = staticmethod(getFileFormats)
|
|
|
54
|
|
|
55
|
|
|
56 def skipFirstLines(self):
|
|
|
57 pass
|
|
|
58
|
|
|
59
|
|
|
60 def getInfos(self):
|
|
|
61 self.chromosomes = set()
|
|
|
62 self.nbMappings = 0
|
|
|
63 self.size = 0
|
|
|
64 cpt = 0
|
|
|
65 self.reset()
|
|
|
66 for line in self.handle:
|
|
|
67 line = line.strip()
|
|
|
68 if line == "": continue
|
|
|
69 if cpt % 3 == 0:
|
|
|
70 line = line.strip()
|
|
|
71 parts = line.split(" ")
|
|
|
72 self.chromosomes.add(parts[1])
|
|
|
73 self.size += int(parts[6])
|
|
|
74 self.nbMappings += 1
|
|
|
75 cpt += 1
|
|
|
76 if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
|
|
|
77 sys.stdout.write(" %d mappings read\r" % (self.nbMappings))
|
|
|
78 sys.stdout.flush()
|
|
|
79 self.reset()
|
|
|
80 if self.verbosity >= 10:
|
|
|
81 print " %d mappings read" % (self.nbMappings)
|
|
|
82 print "Done."
|
|
|
83
|
|
|
84
|
|
|
85 def parseLine(self, line):
|
|
|
86
|
|
|
87 if line.strip() == "":
|
|
|
88 for line in self.handle:
|
|
|
89 self.currentLineNb += 1
|
|
|
90 break
|
|
|
91 if line.strip() == "":
|
|
|
92 return None
|
|
|
93
|
|
|
94 m = re.search(r"^\s*\d+\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s*$", line)
|
|
|
95 if m != None:
|
|
|
96 #sys.exit("\nLine %d '%s' does not have an AXT format" % (self.currentLineNb, line))
|
|
|
97
|
|
|
98 mapping = Mapping()
|
|
|
99 subMapping = SubMapping()
|
|
|
100
|
|
|
101 offset = -1 if m.group(7) == "-" else 0
|
|
|
102 subMapping.queryInterval.setName(m.group(4))
|
|
|
103 subMapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1)
|
|
|
104 subMapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1)
|
|
|
105 subMapping.queryInterval.setDirection(m.group(7))
|
|
|
106
|
|
|
107 subMapping.targetInterval.setChromosome(m.group(1))
|
|
|
108 subMapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset)
|
|
|
109 subMapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset)
|
|
|
110 subMapping.targetInterval.setDirection(1)
|
|
|
111
|
|
|
112 subMapping.setSize(min(subMapping.targetInterval.getSize(), subMapping.queryInterval.getSize()))
|
|
|
113 subMapping.setDirection(m.group(7))
|
|
|
114
|
|
|
115 mapping.addSubMapping(subMapping)
|
|
|
116
|
|
|
117 mapping.setDirection(m.group(7))
|
|
|
118 mapping.targetInterval.setChromosome(m.group(1))
|
|
|
119 mapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset)
|
|
|
120 mapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset)
|
|
|
121
|
|
|
122 mapping.queryInterval.setName(m.group(4))
|
|
|
123 mapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1)
|
|
|
124 mapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1)
|
|
|
125
|
|
|
126 mapping.setSize(min(mapping.targetInterval.getSize(), mapping.queryInterval.getSize()))
|
|
|
127
|
|
|
128 for line in self.handle:
|
|
|
129 string1 = line.strip()
|
|
|
130 self.currentLineNb += 1
|
|
|
131 break
|
|
|
132 for line in self.handle:
|
|
|
133 string2 = line.strip()
|
|
|
134 self.currentLineNb += 1
|
|
|
135 break
|
|
|
136 mapping.setNbMismatches(Utils.getHammingDistance(string1, string2))
|
|
|
137 mapping.setNbGaps(0)
|
|
|
138
|
|
|
139 self.currentMapping = mapping
|
|
|
140 else:
|
|
|
141 if self.queryLine == None:
|
|
|
142 self.queryLine = line
|
|
|
143 else:
|
|
|
144 self.subjectLine = line
|
|
|
145 seqLen = float(len(self.subjectLine))
|
|
|
146 dist = float(getHammingDistance(self.queryLine, self.subjectLine))
|
|
|
147 identity = ((seqLen-dist)/seqLen) *100
|
|
|
148 self.currentMapping.setIdentity(identity)
|
|
|
149 self.queryLine = None
|
|
|
150 self.subjectLine = None
|
|
|
151 return self.currentMapping
|
|
|
152
|
|
|
153
|
|
|
154
|
