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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30 import re
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31 import sys
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32 from SMART.Java.Python.structure.Interval import Interval
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33 from SMART.Java.Python.structure.Transcript import Transcript
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34 from commons.core.parsing.TranscriptListParser import TranscriptListParser
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35
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36
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37 class GbParser(TranscriptListParser):
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38 """A class that parses a GBrowse file and create a transcript list"""
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39
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40
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41 def __init__(self, fileName, verbosity = 0):
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42 self.reference = None
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43 self.color = None
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44 super(GbParser, self).__init__(fileName, verbosity)
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45
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46
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47 def __del__(self):
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48 super(GbParser, self).__del__()
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49
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50
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51 def getFileFormats():
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52 return ["gb", "gbrowse"]
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53 getFileFormats = staticmethod(getFileFormats)
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54
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55
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56 def skipFirstLines(self):
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57 for line in self.handle:
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58 self.currentLineNb += 1
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59 line = line.strip()
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60 m = re.search(r"^\s*bgcolor\s*=\s*(\S+)\s*$", line)
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61 if m != None:
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62 self.color = m.group(1)
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63 if line == "":
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64 return
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65
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66
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67 def parseLine(self, line):
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68 transcript = Transcript()
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69 # first line (reference)
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70 m = re.search(r"^\s*reference\s*=\s*(\S+)\s*$", line)
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71 if m != None:
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72 self.reference = m.group(1)
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73 for line in self.handle:
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74 line = line.strip()
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75 self.currentLineNb += 1
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76 break
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77 # second line (genomic coordinates)
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78 m = re.search(r"^\s*READS\s+(\S+)\s+(\S+)\s+\"([^\"]*)\"\s*$", line)
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79 if m == None:
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80 sys.exit("\nLine %d '%s' does not have a GBrowse format" % (self.currentLineNb, line))
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81 if self.reference == None:
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82 sys.exit("Cannot get reference of GBrowse line %d '%s'" % (self.currentLineNb, line))
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83 transcript.setChromosome(self.reference)
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84 transcript.setName(m.group(1))
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85 transcript.setComment(m.group(3))
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86 # exons
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87 exons = m.group(2).split(",")
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88 transcriptStart = 1000000000
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89 transcriptEnd = 0
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90 direction = 0
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91 for exon in exons:
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92 m = re.search(r"^(\d+)-(\d+)$", exon)
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93 if m == None:
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94 sys.exit("\nCannot read GBrowse exon line %d '%s'" % (self.currentLineNb, exon))
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95 interval = Interval()
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96 interval.setChromosome(transcript.chromosome)
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97 direction += int(m.group(2)) - int(m.group(1))
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98 start = min(int(m.group(1)), int(m.group(2)))
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99 end = max(int(m.group(1)), int(m.group(2)))
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100 interval.setStart(start)
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101 interval.setEnd(end)
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102 transcriptStart = min(transcriptStart, start)
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103 transcriptEnd = max(transcriptEnd, end)
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104 transcript.addExon(interval)
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105 transcript.setStart(transcriptStart)
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106 transcript.setEnd(transcriptEnd)
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107 transcript.setDirection(direction)
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108 for exon in transcript.getExons():
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109 exon.setDirection(direction)
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110 return transcript
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111
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