Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/BlastParser.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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35:d94018ca4ada | 36:44d5973c188c |
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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.Interval import Interval | |
34 from SMART.Java.Python.structure.SubMapping import SubMapping | |
35 from SMART.Java.Python.structure.Mapping import Mapping | |
36 | |
37 | |
38 class BlastParser(MapperParser): | |
39 """A class that parses the output of Blast (-m 8 format)""" | |
40 | |
41 def __init__(self, fileName, verbosity = 0): | |
42 super(BlastParser, self).__init__(fileName, verbosity) | |
43 | |
44 | |
45 def __del__(self): | |
46 super(BlastParser, self).__del__() | |
47 | |
48 | |
49 def getFileFormats(): | |
50 return ["blast"] | |
51 getFileFormats = staticmethod(getFileFormats) | |
52 | |
53 | |
54 def skipFirstLines(self): | |
55 pass | |
56 | |
57 | |
58 def parseLine(self, line): | |
59 m = re.search(r"^(\S+)\s+(\S+)\s+(\d+\.?\d*)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+([-+]?\d+\.?\d*[eE]?[-+]?\d*)\s+(\d+\.?\d*)\s*$", line) | |
60 if m == None: | |
61 sys.exit("\nLine %d '%s' does not have an Blast format" % (self.currentLineNb, line)) | |
62 | |
63 mapping = Mapping() | |
64 | |
65 queryInterval = Interval() | |
66 queryInterval.setName(m.group(1)) | |
67 queryInterval.setStart(min(int(m.group(7)), int(m.group(8)))) | |
68 queryInterval.setEnd(max(int(m.group(7)), int(m.group(8)))) | |
69 | |
70 targetInterval = Interval() | |
71 targetInterval.setChromosome(m.group(2)) | |
72 targetInterval.setStart(min(int(m.group(9)), int(m.group(10)))) | |
73 targetInterval.setEnd(max(int(m.group(9)), int(m.group(10)))) | |
74 | |
75 subMapping = SubMapping() | |
76 subMapping.setQueryInterval(queryInterval) | |
77 subMapping.setTargetInterval(targetInterval) | |
78 | |
79 mapping.addSubMapping(subMapping) | |
80 | |
81 mapping.setIdentity(round(float(m.group(3)))) | |
82 mapping.setSize(int(m.group(4))) | |
83 mapping.setNbMismatches(int(m.group(5))) | |
84 mapping.setNbGaps(int(m.group(6))) | |
85 mapping.setDirection((int(m.group(8)) - int(m.group(7))) * (int(m.group(10)) - int(m.group(9)))) | |
86 mapping.setEvalue(float(m.group(11))) | |
87 | |
88 return mapping |