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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Restrict a transcript list with some parameters (regions)"""
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32
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33 from optparse import OptionParser
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34 from SMART.Java.Python.structure.Transcript import Transcript
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35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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36 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
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37 from commons.core.writer.Gff3Writer import Gff3Writer
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38 from commons.core.parsing.FastaParser import FastaParser
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39 from SMART.Java.Python.misc.Progress import Progress
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40
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41 class DifferenceGetter(object):
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42
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43 def __init__(self, verbosity):
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44 self.verbosity = verbosity
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45 self.annotationParser = None
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46 self.referenceParser = None
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47 self.sequenceParser = None
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48 self.transcriptCount = 1
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49 self.split = False
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50
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51 def createTranscript(self, chromosome, start, end):
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52 transcript = Transcript()
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53 transcript.setChromosome(chromosome)
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54 transcript.setDirection("+")
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55 transcript.setStart(start)
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56 transcript.setEnd(end)
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57 transcript.setName("region_%d" % self.transcriptCount)
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58 transcript.setTagValue("ID", "region_%d" % self.transcriptCount)
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59 self.transcriptCount += 1
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60 return transcript
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61
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62 def setSplit(self, split):
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63 self.split = split
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64
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65 def setAnnotationFile(self, fileName, format):
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66 if fileName != None:
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67 self.annotationParser = TranscriptContainer(fileName, format, self.verbosity)
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68
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69 def setReferenceFile(self, fileName, format):
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70 if fileName != None:
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71 self.referenceParser = TranscriptContainer(fileName, format, self.verbosity)
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72
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73 def setSequenceFile(self, fileName):
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74 if fileName != None:
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75 self.sequenceParser = FastaParser(fileName, self.verbosity)
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76
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77 def setOutputFile(self, fileName):
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78 self.writer = Gff3Writer(fileName, self.verbosity)
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79
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80 def initialize(self):
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81 self.presence = {}
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82 for chromosome in self.sequenceParser.getRegions():
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83 self.presence[chromosome] = [[1, self.sequenceParser.getSizeOfRegion(chromosome)]]
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84
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85 def readTranscripts(self):
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86 nbTranscripts = self.annotationParser.getNbTranscripts()
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87 progress = Progress(nbTranscripts, "Parsing annotation file" , self.verbosity)
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88 for transcript in self.annotationParser.getIterator():
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89 chromosome = transcript.getChromosome()
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90 toBeDeleted = []
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91 toBeAppended = []
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92 for i, element in enumerate(self.presence[chromosome]):
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93 start, end = element
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94 if start <= transcript.getEnd() and transcript.getStart() <= end:
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95 toBeDeleted.append(i)
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96 if start < transcript.getStart():
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97 toBeAppended.append([start, transcript.getStart() - 1])
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98 if end > transcript.getEnd():
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99 toBeAppended.append([transcript.getEnd() + 1, end])
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100 for i in reversed(toBeDeleted):
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101 del self.presence[chromosome][i]
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102 self.presence[chromosome].extend(toBeAppended)
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103 progress.inc()
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104 progress.done()
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105
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106 def writeOutput(self):
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107 for chromosome in self.presence:
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108 for element in self.presence[chromosome]:
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109 start, end = element
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110 self.writer.addTranscript(self.createTranscript(chromosome, start, end))
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111 self.writer.write()
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112
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113 def compareToSequence(self):
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114 self.initialize()
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115 self.readTranscripts()
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116 self.writeOutput()
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117
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118 def compareToAnnotation(self):
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119 transcriptListComparator = TranscriptListsComparator(None, self.verbosity)
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120 transcriptListComparator.setSplitDifference(self.split)
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121 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, self.annotationParser)
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122 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, self.referenceParser)
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123 transcriptListComparator.setOutputWriter(self.writer)
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124 transcriptListComparator.getDifferenceTranscriptList()
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125
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126 def run(self):
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127 if self.referenceParser != None:
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128 self.compareToAnnotation()
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129 else:
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130 self.compareToSequence()
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131
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132
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133 if __name__ == "__main__":
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134
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135 # parse command line
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136 description = "Get Difference v1.0.1: Get all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level). [Category: Data Comparison]"
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137
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138 parser = OptionParser(description = description)
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139 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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140 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format [compulsory] [format: transcript file format]")
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141 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", default=None, type="string", help="reference file [format: file in transcript format given by -g]")
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142 parser.add_option("-g", "--format2", dest="format2", action="store", default=None, type="string", help="format of the reference file [format: transcript file format]")
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143 parser.add_option("-s", "--sequence", dest="sequenceFileName", action="store", default=None, type="string", help="sequence file [format: file in FASTA format]")
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144 parser.add_option("-p", "--split", dest="split", action="store_true", default=False, help="when comparing to a set of genomic coordinates, do not join [format: boolean] [default: False")
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145 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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146 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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147 (options, args) = parser.parse_args()
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148
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149 getter = DifferenceGetter(options.verbosity)
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150 getter.setSplit(options.split)
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151 getter.setAnnotationFile(options.inputFileName1, options.format1)
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152 getter.setSequenceFile(options.sequenceFileName)
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153 getter.setReferenceFile(options.inputFileName2, options.format2)
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154 getter.setOutputFile(options.outputFileName)
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155 getter.run()
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