Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/GbParser.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 SMART.Java.Python.structure.Interval import Interval | |
33 from SMART.Java.Python.structure.Transcript import Transcript | |
34 from commons.core.parsing.TranscriptListParser import TranscriptListParser | |
35 | |
36 | |
37 class GbParser(TranscriptListParser): | |
38 """A class that parses a GBrowse file and create a transcript list""" | |
39 | |
40 | |
41 def __init__(self, fileName, verbosity = 0): | |
42 self.reference = None | |
43 self.color = None | |
44 super(GbParser, self).__init__(fileName, verbosity) | |
45 | |
46 | |
47 def __del__(self): | |
48 super(GbParser, self).__del__() | |
49 | |
50 | |
51 def getFileFormats(): | |
52 return ["gb", "gbrowse"] | |
53 getFileFormats = staticmethod(getFileFormats) | |
54 | |
55 | |
56 def skipFirstLines(self): | |
57 for line in self.handle: | |
58 self.currentLineNb += 1 | |
59 line = line.strip() | |
60 m = re.search(r"^\s*bgcolor\s*=\s*(\S+)\s*$", line) | |
61 if m != None: | |
62 self.color = m.group(1) | |
63 if line == "": | |
64 return | |
65 | |
66 | |
67 def parseLine(self, line): | |
68 transcript = Transcript() | |
69 # first line (reference) | |
70 m = re.search(r"^\s*reference\s*=\s*(\S+)\s*$", line) | |
71 if m != None: | |
72 self.reference = m.group(1) | |
73 for line in self.handle: | |
74 line = line.strip() | |
75 self.currentLineNb += 1 | |
76 break | |
77 # second line (genomic coordinates) | |
78 m = re.search(r"^\s*READS\s+(\S+)\s+(\S+)\s+\"([^\"]*)\"\s*$", line) | |
79 if m == None: | |
80 sys.exit("\nLine %d '%s' does not have a GBrowse format" % (self.currentLineNb, line)) | |
81 if self.reference == None: | |
82 sys.exit("Cannot get reference of GBrowse line %d '%s'" % (self.currentLineNb, line)) | |
83 transcript.setChromosome(self.reference) | |
84 transcript.setName(m.group(1)) | |
85 transcript.setComment(m.group(3)) | |
86 # exons | |
87 exons = m.group(2).split(",") | |
88 transcriptStart = 1000000000 | |
89 transcriptEnd = 0 | |
90 direction = 0 | |
91 for exon in exons: | |
92 m = re.search(r"^(\d+)-(\d+)$", exon) | |
93 if m == None: | |
94 sys.exit("\nCannot read GBrowse exon line %d '%s'" % (self.currentLineNb, exon)) | |
95 interval = Interval() | |
96 interval.setChromosome(transcript.chromosome) | |
97 direction += int(m.group(2)) - int(m.group(1)) | |
98 start = min(int(m.group(1)), int(m.group(2))) | |
99 end = max(int(m.group(1)), int(m.group(2))) | |
100 interval.setStart(start) | |
101 interval.setEnd(end) | |
102 transcriptStart = min(transcriptStart, start) | |
103 transcriptEnd = max(transcriptEnd, end) | |
104 transcript.addExon(interval) | |
105 transcript.setStart(transcriptStart) | |
106 transcript.setEnd(transcriptEnd) | |
107 transcript.setDirection(direction) | |
108 for exon in transcript.getExons(): | |
109 exon.setDirection(direction) | |
110 return transcript | |
111 |