Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/MummerParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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.Mapping import Mapping | |
34 from SMART.Java.Python.structure.SubMapping import SubMapping | |
35 | |
36 class MummerParser(MapperParser): | |
37 """A class that parses the output of Mummer format""" | |
38 | |
39 def __init__(self, fileName, verbosity = 0): | |
40 super(MummerParser, self).__init__(fileName, verbosity) | |
41 | |
42 | |
43 def __del__(self): | |
44 super(MummerParser, self).__del__() | |
45 | |
46 | |
47 def getFileFormats(): | |
48 return ["mummer"] | |
49 getFileFormats = staticmethod(getFileFormats) | |
50 | |
51 | |
52 def skipFirstLines(self): | |
53 pass | |
54 | |
55 | |
56 def parseLine(self, line): | |
57 mapping = Mapping() | |
58 | |
59 subMapping = SubMapping() | |
60 | |
61 # handle header | |
62 m = re.search(r"^>\s+(\S+)\s+Reverse\s+Len\s+=\s+(\d+)$", line) | |
63 if m != None: | |
64 subMapping.queryInterval.setName(m.group(1)) | |
65 subMapping.queryInterval.setSize(int(m.group(2))) | |
66 subMapping.queryInterval.setDirection(-1) | |
67 else: | |
68 m = re.search(r"^>\s+(\S+)\s+Len\s+=\s+(\d+)$", line) | |
69 if m != None: | |
70 subMapping.queryInterval.setName(m.group(1)) | |
71 subMapping.queryInterval.setSize(int(m.group(2))) | |
72 subMapping.queryInterval.setDirection(1) | |
73 else : | |
74 sys.exit("Header line %d '%s' is strange in Mummer file" % (self.currentLineNb, line)) | |
75 | |
76 for line in self.handle: | |
77 self.currentLineNb += 1 | |
78 break | |
79 line = line.strip() | |
80 | |
81 # handle line | |
82 m = re.search(r"^(\w+)\s+(\d+)\s+(\d+)\s+(\d+)$", line) | |
83 if m != None: | |
84 subMapping.targetInterval.setName(m.group(1)) | |
85 subMapping.targetInterval.setStart(int(m.group(2))) | |
86 subMapping.queryInterval.setStart(int(m.group(3))) | |
87 subMapping.targetInterval.setSize(int(m.group(4))) | |
88 else: | |
89 sys.exit("Line %d '%s' is strange in Mummer file" % (self.currentLineNb, line)) | |
90 | |
91 mapping.addSubMapping(subMapping) | |
92 | |
93 return mapping |