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