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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 GffParser(TranscriptListParser):
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38 """A class that parses a GFF 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 super(GffParser, self).__init__(fileName, verbosity)
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43
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44
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45 def __del__(self):
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46 super(GffParser, self).__del__()
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47
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48
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49 def getFileFormats():
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50 return ["gff", "gff2", "gff3"]
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51 getFileFormats = staticmethod(getFileFormats)
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52
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53
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54 def skipFirstLines(self):
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55 pass
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56
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57
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58 def getInfos(self):
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59 self.chromosomes = set()
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60 self.nbTranscripts = 0
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61 self.size = 0
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62 self.reset()
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63 if self.verbosity >= 10:
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64 print "Getting information on %s." % (self.fileName)
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65 self.reset()
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66 for line in self.handle:
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67 line = line.strip()
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68 if line == "" or line[0] == "#":
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69 continue
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70 parts = line.split("\t")
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71 if len(parts) != 9:
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72 raise Exception("Error! Line '%s' has %d tab-separated fields instead of 9!" % (line, len(parts)))
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73 self.chromosomes.add(parts[0])
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74 if parts[8].find("Parent") == -1:
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75 self.nbTranscripts += 1
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76 else:
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77 self.size += max(int(parts[3]), int(parts[4])) - min(int(parts[3]), int(parts[4])) + 1
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78 if self.verbosity >= 10 and self.nbTranscripts % 100000 == 0:
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79 sys.stdout.write(" %d transcripts read\r" % (self.nbTranscripts))
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80 sys.stdout.flush()
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81 self.reset()
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82 if self.verbosity >= 10:
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83 print " %d transcripts read" % (self.nbTranscripts)
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84 print "Done."
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85
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86
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87 def parseLine(self, line):
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88 if not line or line[0] == "#":
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89 return None
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90 m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([+-.])\s+(\S+)\s+(\S.*)$", line)
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91 if m == None:
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92 raise Exception("\nLine %d '%s' does not have a GFF format\n" % (self.currentLineNb, line))
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93 interval = Interval()
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94 interval.setChromosome(m.group(1))
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95 interval.setName("unnamed transcript")
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96 interval.setStart(min(int(m.group(4)), int(m.group(5))))
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97 interval.setEnd(max(int(m.group(4)), int(m.group(5))))
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98 if m.group(7) == ".":
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99 interval.setDirection("+")
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100 else:
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101 interval.setDirection(m.group(7))
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102 interval.setTagValue("feature", m.group(3))
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103 if m.group(6).isdigit():
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104 interval.setTagValue("score", m.group(6))
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105
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106 remainings = m.group(9).split(";")
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107 for remaining in remainings:
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108 remaining = remaining.strip()
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109 if remaining == "":
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110 continue
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111 posSpace = remaining.find(" ")
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112 posEqual = remaining.find("=")
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113 if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
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114 parts = remaining.split("=")
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115 else:
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116 parts = remaining.split()
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117 field = parts[0].strip()
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118 value = " ".join(parts[1:]).strip(" \"")
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119 if field in ("Name", "name", "Sequence", "TE", "SAT"):
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120 interval.setName(value)
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121 else:
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122 try:
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123 intValue = int(value)
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124 interval.setTagValue(field, intValue)
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125 except ValueError:
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126 interval.setTagValue(field, value)
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127
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128 self.currentTranscriptAddress = self.previousTranscriptAddress
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129 if "Parent" in interval.getTagNames():
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130 if self.currentTranscript == None:
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131 raise Exception("GFF file does not start with a transcript! First line is '%s'." % (line.strip()))
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132 if interval.getTagValue("Parent") != self.currentTranscript.getTagValue("ID"):
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133 raise Exception("Exon '%s' is not right after its transcript in GFF file!" % (interval))
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134 self.currentTranscript.addExon(interval)
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135 if interval.name == None:
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136 interval.name = self.currentTranscript.name
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137 return None
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138
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139 transcript = self.currentTranscript
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140 self.currentTranscript = Transcript()
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141 self.currentTranscript.copy(interval)
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142 self.previousTranscriptAddress = self.currentAddress
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143
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144 if transcript != None and transcript.name.startswith("unnamed"):
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145 if "ID" in transcript.getTagNames():
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146 transcript.name = transcript.getTagValue("ID")
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147 else:
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148 transcript.name = "unnamed transcript %s" % (self.currentLineNb)
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149 return transcript
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