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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 import os
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32 from optparse import OptionParser, OptionGroup
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33 from commons.core.parsing.ParserChooser import ParserChooser
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34 from commons.core.writer.Gff3Writer import Gff3Writer
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
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37 from SMART.Java.Python.ncList.FileSorter import FileSorter
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38 from SMART.Java.Python.misc.Progress import Progress
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39
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40
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41 class CollapseReads(object):
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42 """
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43 Merge two reads if they have exactly the same genomic coordinates
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44 """
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45
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46 def __init__(self, verbosity = 0):
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47 self.verbosity = verbosity
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48 self.inputReader = None
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49 self.outputWriter = None
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50 self.strands = True
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51 self.nbRead = 0
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52 self.nbWritten = 0
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53 self.nbMerges = 0
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54 self.splittedFileNames = {}
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55
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56 def __del__(self):
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57 for fileName in self.splittedFileNames.values():
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58 os.remove(fileName)
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59
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60 def close(self):
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61 self.outputWriter.close()
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62
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63 def setInputFile(self, fileName, format):
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64 parserChooser = ParserChooser(self.verbosity)
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65 parserChooser.findFormat(format)
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66 self.parser = parserChooser.getParser(fileName)
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67 self.sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
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68
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69 def setOutputFile(self, fileName):
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70 self.outputWriter = Gff3Writer(fileName, self.verbosity)
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71
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72 def getNbElements(self):
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73 return self.parser.getNbTranscripts()
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74
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75 def _sortFile(self):
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76 fs = FileSorter(self.parser, self.verbosity-4)
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77 fs.perChromosome(True)
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78 fs.setOutputFileName(self.sortedFileName)
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79 fs.sort()
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80 self.splittedFileNames = fs.getOutputFileNames()
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81 self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
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82 self.nbRead = fs.getNbElements()
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83
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84 def _iterate(self, chromosome):
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85 progress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
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86 transcripts = []
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87 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
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88 for newTranscript in parser.getIterator():
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89 newTranscripts = []
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90 for oldTranscript in transcripts:
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91 if self._checkOverlap(newTranscript, oldTranscript):
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92 self._merge(newTranscript, oldTranscript)
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93 elif self._checkPassed(newTranscript, oldTranscript):
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94 self._write(oldTranscript)
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95 else:
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96 newTranscripts.append(oldTranscript)
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97 newTranscripts.append(newTranscript)
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98 transcripts = newTranscripts
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99 progress.inc()
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100 for transcript in transcripts:
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101 self._write(transcript)
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102 progress.done()
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103
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104 def _merge(self, transcript1, transcript2):
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105 self.nbMerges += 1
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106 transcript2.setDirection(transcript1.getDirection())
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107 transcript1.merge(transcript2)
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108
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109 def _write(self, transcript):
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110 self.nbWritten += 1
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111 self.outputWriter.addTranscript(transcript)
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112
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113 def _checkOverlap(self, transcript1, transcript2):
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114 if transcript1.getStart() != transcript2.getStart() or transcript1.getEnd() != transcript2.getEnd():
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115 return False
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116 return (not self.strands or transcript1.getDirection() == transcript2.getDirection())
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117
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118 def _checkPassed(self, transcript1, transcript2):
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119 return (transcript2.getStart() < transcript1.getStart())
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120
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121 def collapseChromosome(self, chromosome):
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122 progress = Progress(table.getNbElements(), "Analysing chromosome %s" % (chromosome), self.verbosity)
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123 command = "SELECT * FROM %s ORDER BY start ASC, end DESC" % (table.name)
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124 transcriptStart = None
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125 transcriptEnd = None
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126 transcriptDirection = None
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127 currentTranscript = None
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128 if self.strands:
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129 command += ", direction"
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130 for index, transcript in table.selectTranscripts(command, True):
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131 self.nbRead += 1
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132 if not self.strands:
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133 transcript.setDirection("+")
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134 if transcriptStart != transcript.getStart() or transcriptEnd != transcript.getEnd() or transcriptDirection != transcript.getDirection():
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135 self.writeTranscript(currentTranscript)
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136 transcriptStart = transcript.getStart()
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137 transcriptEnd = transcript.getEnd()
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138 transcriptDirection = transcript.getDirection()
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139 currentTranscript = transcript
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140 else:
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141 currentTranscript.setTagValue("nbElements", (currentTranscript.getTagValue("nbElements") + 1) if "nbElements" in currentTranscript.getTagNames() else 1)
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142 progress.inc()
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143 self.writeTranscript(currentTranscript)
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144 progress.done()
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145
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146 def collapse(self):
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147 self._sortFile()
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148 for chromosome in sorted(self.nbElementsPerChromosome.keys()):
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149 self._iterate(chromosome)
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150 self.outputWriter.close()
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151 if self.verbosity > 1:
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152 print "# reads read: %d" % (self.nbRead)
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153 print "# reads written: %d (%.2f%%)" % (self.nbWritten, float(self.nbWritten) / self.nbRead * 100)
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154 print "# reads merges: %d" % (self.nbMerges)
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155
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156 if __name__ == "__main__":
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157
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158 # parse command line
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159 description = "Collapse Reads v1.0.3: Merge two reads if they have exactly the same genomic coordinates. [Category: Merge]"
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160
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161 parser = OptionParser(description = description)
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162 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
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163 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the file [compulsory] [format: mapping file format]")
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164 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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165 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="merge elements on 2 different strands [format: bool] [default: false]")
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166 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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167 (options, args) = parser.parse_args()
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168
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169 collapser = CollapseReads(options.verbosity)
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170 collapser.setInputFile(options.inputFileName, options.format)
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171 collapser.setOutputFile(options.outputFileName)
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172 collapser.strands = not options.strands
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173 collapser.collapse()
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174 collapser.close()
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