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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2012
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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 from SMART.Java.Python.misc import Utils
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40
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41
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42 class GetUpDownStream(object):
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43
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44 def __init__(self, verbosity = 0):
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45 self.verbosity = verbosity
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46 self.inputReader = None
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47 self.outputWriter = None
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48 self.nbRead = 0
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49 self.nbWritten = 0
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50 self.nbMerges = 0
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51 self.splittedFileNames = {}
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52
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53 def __del__(self):
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54 for fileName in self.splittedFileNames.values():
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55 os.remove(fileName)
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56
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57 def setInputFile(self, fileName, format):
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58 parserChooser = ParserChooser(self.verbosity)
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59 parserChooser.findFormat(format, "transcript")
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60 self.parser = parserChooser.getParser(fileName)
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61 self.sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
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62
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63 def setOutputFile(self, fileName):
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64 self.outputWriter = Gff3Writer(fileName, self.verbosity)
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65
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66 def setDistances(self, up, down):
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67 self.upDistance = up
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68 self.downDistance = down
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69
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70 def _sortFile(self):
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71 fs = FileSorter(self.parser, self.verbosity-4)
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72 fs.perChromosome(True)
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73 fs.setOutputFileName(self.sortedFileName)
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74 fs.sort()
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75 self.splittedFileNames = fs.getOutputFileNames()
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76 self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
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77 self.nbRead = fs.getNbElements()
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78
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79 def _write(self, start, end, reference, after):
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80 if start > end:
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81 return
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82 transcript = Transcript()
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83 transcript.setChromosome(reference.getChromosome())
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84 transcript.setStart(start)
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85 transcript.setEnd(end)
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86 transcript.setDirection("+")
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87 transcript.setName("%s_%s" % ("up" if Utils.xor(reference.getDirection() == 1, after) else "down", reference.getName()))
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88 self.outputWriter.addTranscript(transcript)
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89
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90 def _getFlanking(self, chromosome):
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91 progress = Progress(self.nbElementsPerChromosome[chromosome], "Analyzing chromosome %s" % (chromosome), self.verbosity)
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92 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
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93 previous = None
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94 for transcript in parser.getIterator():
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95 progress.inc()
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96 transcript.removeExons()
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97 if previous == None:
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98 distance = self.upDistance if transcript.getDirection() == 1 else self.downDistance
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99 start = max(1, transcript.getStart() - distance)
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100 self._write(start, transcript.getStart()-1, transcript, False)
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101 previous = transcript
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102 continue
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103 if previous.include(transcript):
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104 continue
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105 if transcript.overlapWith(previous):
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106 previous = transcript
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107 continue
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108 distancePrevious = self.downDistance if previous.getDirection() == 1 else self.upDistance
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109 distanceCurrent = self.upDistance if transcript.getDirection() == 1 else self.downDistance
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110 distance = transcript.getDistance(previous)
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111 if distancePrevious + distanceCurrent == 0:
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112 previous = transcript
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113 continue
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114 if distance >= distancePrevious + distanceCurrent:
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115 endPrevious = previous.getEnd() + distancePrevious
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116 startCurrent = transcript.getStart() - distanceCurrent
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117 else:
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118 middle = previous.getEnd() + int((distance-1) * float(distancePrevious) / (distancePrevious + distanceCurrent))
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119 endPrevious = middle
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120 startCurrent = middle+1
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121 self._write(previous.getEnd() + 1, endPrevious, previous, True)
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122 self._write(startCurrent, transcript.getStart() - 1, transcript, False)
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123 previous = transcript
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124 distance = self.downDistance if previous.getDirection() == 1 else self.upDistance
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125 self._write(previous.getEnd() + 1, previous.getEnd() + distance, previous, True)
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126 progress.done()
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127
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128 def run(self):
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129 self._sortFile()
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130 for chromosome in sorted(self.nbElementsPerChromosome.keys()):
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131 self._getFlanking(chromosome)
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132 self.outputWriter.close()
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133
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134 if __name__ == "__main__":
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135
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136 # parse command line
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137 description = "Get Up and Down Stream v1.0.0: Get the flanking regions of an annotation. [Category: Data Modification]"
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138
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139 parser = OptionParser(description = description)
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140 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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141 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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142 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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143 parser.add_option("-u", "--up", dest="up", action="store", default=0, type="int", help="the upstream distance [format: int]")
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144 parser.add_option("-d", "--down", dest="down", action="store", default=0, type="int", help="the downstream distance [format: int]")
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145 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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146 (options, args) = parser.parse_args()
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147
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148 guds = GetUpDownStream(options.verbosity)
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149 guds.setInputFile(options.inputFileName, options.format)
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150 guds.setOutputFile(options.outputFileName)
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151 guds.setDistances(options.up, options.down)
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152 guds.run()
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