Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/BedParser.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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 commons.core.parsing.TranscriptListParser import TranscriptListParser | |
34 from SMART.Java.Python.structure.Transcript import Transcript | |
35 | |
36 | |
37 class BedParser(TranscriptListParser): | |
38 """A class that parses a BED file and create a transcript list""" | |
39 | |
40 | |
41 def __init__(self, fileName, verbosity = 0): | |
42 self.title = None | |
43 TranscriptListParser.__init__(self, fileName, verbosity) | |
44 | |
45 | |
46 # def __del__(self): | |
47 # super(BedParser, self).__del__() | |
48 | |
49 | |
50 def getFileFormats(): | |
51 return ["bed"] | |
52 getFileFormats = staticmethod(getFileFormats) | |
53 | |
54 | |
55 def skipFirstLines(self): | |
56 mark = self.handle.tell() | |
57 line = self.handle.readline() | |
58 line = line.strip() | |
59 m = re.search(r"^\s*track\s+name\s*=\s*(\S+)\s+", line) | |
60 if m != None: | |
61 self.title = m.group(1) | |
62 self.currentLineNb += 1 | |
63 else: | |
64 self.handle.seek(mark) | |
65 return | |
66 | |
67 | |
68 | |
69 | |
70 def parseLine(self, line): | |
71 m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\s*$", line) | |
72 if m != None: | |
73 transcript = Transcript() | |
74 transcript.setChromosome(m.group(1)) | |
75 transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) | |
76 transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) | |
77 transcript.setName("Unnamed") | |
78 transcript.setDirection(1) | |
79 return transcript | |
80 | |
81 m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\s*$", line) | |
82 if m != None: | |
83 transcript = Transcript() | |
84 transcript.setChromosome(m.group(1)) | |
85 transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) | |
86 transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) | |
87 transcript.setName(m.group(4)) | |
88 transcript.setDirection(1) | |
89 return transcript | |
90 | |
91 m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+\d+\.?\d*\s*$", line) | |
92 if m != None: | |
93 transcript = Transcript() | |
94 transcript.setChromosome(m.group(1)) | |
95 transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) | |
96 transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) | |
97 transcript.setName(m.group(4)) | |
98 transcript.setDirection(1) | |
99 return transcript | |
100 | |
101 m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+\d+\t+([+-])\t+\d+\t+\d+\t+0\t+(\d+)\t+(\S+)\t+(\S+)\s*$", line) | |
102 if m == None: | |
103 raise Exception("\nLine %d '%s' does not has a BED format." % (self.currentLineNb, line)) | |
104 transcript = Transcript() | |
105 transcript.setChromosome(m.group(1)) | |
106 transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) | |
107 transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) | |
108 transcript.setName(m.group(4)) | |
109 transcript.setDirection(m.group(5)) | |
110 nbExons = int(m.group(6)) | |
111 sizes = m.group(7).split(",") | |
112 starts = m.group(8).split(",") | |
113 | |
114 # check for comment in name | |
115 m = re.search(r"^([^\(]*)\((\S+)\)$", transcript.getName()) | |
116 if m != None: | |
117 transcript.setName(m.group(1)) | |
118 transcript.setTagValues(m.group(2), ";", "=") | |
119 | |
120 # check for nb occurrences in name | |
121 m = re.search(r"(.*)-(\d+)$", transcript.getName()) | |
122 if m != None: | |
123 transcript.setName(m.group(1)) | |
124 transcript.setOccurrence(int(m.group(2))) | |
125 | |
126 for i in range(nbExons): | |
127 exon = Interval(transcript) | |
128 exon.setStart(int(starts[i])+transcript.getStart()) | |
129 exon.setEnd(transcript.getStart()+int(starts[i])+int(sizes[i])-1) | |
130 exon.setSize(int(sizes[i])) | |
131 transcript.addExon(exon) | |
132 | |
133 if transcript.exons[0].getStart() != transcript.getStart(): | |
134 sys.exit("There is something wrong with the start of transcript line '%s': transcript starts at %d whereas first exon starts at %d" % (line.strip(), transcript.start, transcript.exons[0].start)) | |
135 if transcript.exons[-1].getEnd() != transcript.getEnd(): | |
136 sys.exit("There is something wrong with the end of transcript line '%s': transcript ends at %d whereas last exon ends at %d" % (line.strip(), transcript.end, transcript.exons[-1].end)) | |
137 | |
138 return transcript | |
139 |