Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/AxtParser.py @ 36:44d5973c188c
Uploaded
author | m-zytnicki |
---|---|
date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
35:d94018ca4ada | 36:44d5973c188c |
---|---|
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 mapping = Mapping() | |
97 subMapping = SubMapping() | |
98 | |
99 subMapping.queryInterval.setName(m.group(4)) | |
100 subMapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))) | |
101 subMapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))) | |
102 subMapping.queryInterval.setDirection(m.group(7)) | |
103 | |
104 subMapping.targetInterval.setChromosome(m.group(1)) | |
105 subMapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3)))) | |
106 subMapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3)))) | |
107 subMapping.targetInterval.setDirection(1) | |
108 | |
109 subMapping.setSize(min(subMapping.targetInterval.getSize(), subMapping.queryInterval.getSize())) | |
110 subMapping.setDirection(m.group(7)) | |
111 | |
112 mapping.addSubMapping(subMapping) | |
113 | |
114 mapping.setDirection(m.group(7)) | |
115 mapping.targetInterval.setChromosome(m.group(1)) | |
116 mapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3)))) | |
117 mapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3)))) | |
118 | |
119 mapping.queryInterval.setName(m.group(4)) | |
120 mapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))) | |
121 mapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))) | |
122 | |
123 mapping.setSize(min(mapping.targetInterval.getSize(), mapping.queryInterval.getSize())) | |
124 | |
125 self.currentMapping = mapping | |
126 return None | |
127 if self.queryLine == None: | |
128 self.queryLine = line | |
129 return None | |
130 self.subjectLine = line | |
131 seqLen = float(len(self.subjectLine)) | |
132 dist = float(getHammingDistance(self.queryLine, self.subjectLine)) | |
133 self.currentMapping.setNbMismatches(getHammingDistance(self.queryLine, self.subjectLine)) | |
134 self.currentMapping.setNbGaps(0) | |
135 self.queryLine = None | |
136 self.subjectLine = None | |
137 return self.currentMapping | |
138 | |
139 | |
140 |