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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2011
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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 from optparse import OptionParser
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32 from commons.core.parsing.ParserChooser import ParserChooser
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33 from commons.core.writer.TranscriptWriter import TranscriptWriter
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34 from SMART.Java.Python.structure.Interval import Interval
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.structure.Mapping import Mapping
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37 from SMART.Java.Python.misc.Progress import Progress
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38 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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39
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40 MINBIN = 3
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41 MAXBIN = 7
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42 REFERENCE = 0
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43 QUERY = 1
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44
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45 def getBin(start, end):
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46 for i in range(MINBIN, MAXBIN + 1):
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47 binLevel = 10 ** i
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48 if int(start / binLevel) == int(end / binLevel):
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49 return int(i * 10 ** (MAXBIN + 1) + int(start / binLevel))
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50 return int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
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51
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52 def getOverlappingBins(start, end):
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53 array = []
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54 bigBin = int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
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55 for i in range(MINBIN, MAXBIN + 1):
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56 binLevel = 10 ** i
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57 array.append((int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)), int(i * 10 ** (MAXBIN + 1) + int(end / binLevel))))
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58 array.append((bigBin, bigBin))
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59 return array
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60
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61
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62 class CompareOverlappingSmallRef(object):
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63
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64 def __init__(self, verbosity):
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65 self.verbosity = verbosity
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66 self.tableNames = {}
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67 self.nbQueries = 0
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68 self.nbRefs = 0
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69 self.nbWritten = 0
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70 self.nbOverlaps = 0
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71 self.invert = False
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72 self.antisense = False
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73 self.collinear = False
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74 self.distance = None
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10
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75 self.minOverlap = False
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76 self.pcOverlapQuery = False
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77 self.pcOverlapRef = False
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78 self.included = False
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79 self.including = False
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6
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80 self.bins = {}
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81 self.notOverlapping = False
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82
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83 def setReferenceFile(self, fileName, format):
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84 chooser = ParserChooser(self.verbosity)
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85 chooser.findFormat(format)
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86 self.refParser = chooser.getParser(fileName)
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87
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88 def setQueryFile(self, fileName, format):
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89 chooser = ParserChooser(self.verbosity)
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90 chooser.findFormat(format)
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91 self.queryParser = chooser.getParser(fileName)
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92
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93 def setOutputFile(self, fileName):
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94 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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95
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96 def setDistance(self, distance):
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97 self.distance = distance
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98
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99 def setCollinear(self, boolean):
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100 self.collinear = boolean
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101
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102 def setAntisense(self, boolean):
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103 self.antisense = boolean
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104
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105 def setInvert(self, boolean):
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106 self.invert = boolean
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107
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10
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108 def setMinPercentOverlap(self, pcOverlapQuery, pcOverlapRef):
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109 self.pcOverlapQuery = pcOverlapQuery
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110 self.pcOverlapRef = pcOverlapRef
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111
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112 def setInclude(self, included, including):
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113 self.included = included
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114 self.including = including
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115
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6
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116 def includeNotOverlapping(self, boolean):
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117 self.notOverlapping = boolean
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118
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119 def loadRef(self):
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120 progress = UnlimitedProgress(10000, "Reading references", self.verbosity)
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121 for transcript in self.refParser.getIterator():
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122 if transcript.__class__.__name__ == "Mapping":
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123 transcript = transcript.getTranscript()
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124 transcript = self._alterTranscript(transcript, REFERENCE)
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125 chromosome = transcript.getChromosome()
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126 bin = getBin(transcript.getStart(), transcript.getEnd())
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127 if chromosome not in self.bins:
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128 self.bins[chromosome] = {}
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129 if bin not in self.bins[chromosome]:
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130 self.bins[chromosome][bin] = []
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131 self.bins[chromosome][bin].append(transcript)
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132 self.nbRefs += 1
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133 progress.inc()
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134 progress.done()
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135
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136 def _alterTranscript(self, transcript, type):
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137 if type == REFERENCE:
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138 if self.distance != None:
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139 transcript.extendExons(self.distance)
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140 return transcript
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141
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142 def _compareTwoTranscripts(self, queryTranscript, refTranscript):
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143 if not queryTranscript.overlapWithExon(refTranscript):
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144 return False
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145 if self.collinear and queryTranscript.getDirection() != refTranscript.getDirection():
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146 return False
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147 if self.antisense and queryTranscript.getDirection() == refTranscript.getDirection():
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148 return False
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10
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149 if self.included and not queryTranscript.isIncluded(refTranscript):
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150 return False
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151 if self.including and not refTranscript.isIncluded(queryTranscript):
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152 return False
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153 querySize = queryTranscript.getSize()
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154 if self.pcOverlapQuery and not queryTranscript.overlapWithExon(refTranscript, int(querySize * self.pcOverlapQuery / 100.0)):
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155 return False
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156 refSize = refTranscript.getSize()
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157 if self.pcOverlapRef and not queryTranscript.overlapWithExon(refTranscript, int(refSize * self.pcOverlapRef / 100.0)):
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158 return False
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159 if self.minOverlap and not queryTranscript.overlapWithExon(refTranscript, self.minOverlap):
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160 return False
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6
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161 return True
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162
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163 def _compareTranscript(self, queryTranscript):
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164 queryChromosome = queryTranscript.getChromosome()
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165 if queryChromosome not in self.bins:
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166 return []
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167 queryStart = queryTranscript.getStart()
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168 queryEnd = queryTranscript.getEnd()
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169 bins = getOverlappingBins(queryStart, queryEnd)
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170 overlaps = {}
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171 for binRange in bins:
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172 for bin in range(binRange[0], binRange[1]+1):
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173 if bin not in self.bins[queryChromosome]:
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174 continue
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175 for refTranscript in self.bins[queryChromosome][bin]:
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176 if self._compareTwoTranscripts(queryTranscript, refTranscript):
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177 nbElements = int(float(refTranscript.getTagValue("nbElements"))) if "nbElements" in refTranscript.getTagNames() else 1
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178 overlaps[refTranscript.getName()] = int(float(refTranscript.getTagValue("nbElements"))) if "nbElements" in refTranscript.getTagNames() else 1
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179 self.nbOverlaps += nbElements
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180 return overlaps
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181
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182 def _updateTranscript(self, queryTranscript, overlaps):
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183 queryTranscript.setTagValue("nbOverlaps", sum(overlaps.values()))
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184 if overlaps:
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185 queryTranscript.setTagValue("overlapsWith", "--".join(overlaps.keys())[:100])
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186 return queryTranscript
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187
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188 def compare(self):
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189 progress = UnlimitedProgress(10000, "Comparing queries", self.verbosity)
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190 for queryTranscript in self.queryParser.getIterator():
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191 if queryTranscript.__class__.__name__ == "Mapping":
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192 queryTranscript = queryTranscript.getTranscript()
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193 progress.inc()
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194 self.nbQueries += 1
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195 overlaps = self._compareTranscript(queryTranscript)
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196 if self.notOverlapping or (overlaps and not self.invert) or (not overlaps and self.invert):
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197 if not self.invert:
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198 queryTranscript = self._updateTranscript(queryTranscript, overlaps)
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199 self.writer.addTranscript(queryTranscript)
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200 self.nbWritten += 1
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201 progress.done()
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202 self.writer.close()
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203
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204 def displayResults(self):
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10
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205 if self.verbosity > 0:
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206 print "# queries: %d" % (self.nbQueries)
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207 print "# refs: %d" % (self.nbRefs)
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208 print "# written: %d (%d overlaps)" % (self.nbWritten, self.nbOverlaps)
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6
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209
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210 def run(self):
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211 self.loadRef()
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212 self.compare()
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213 self.displayResults()
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214
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215 if __name__ == "__main__":
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216
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217 description = "Compare Overlapping Small Reference v1.0.1: Provide the queries that overlap with a reference, when the reference is small. [Category: Data Comparison]"
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218
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219 parser = OptionParser(description = description)
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10
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220 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
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221 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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222 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
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223 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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224 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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225 parser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False, help="also output not overlapping data [format: bool] [default: false]")
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226 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="accept some distance between query and reference [format: int]")
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227 parser.add_option("-c", "--collinear", dest="collinear", action="store_true", default=False, help="provide collinear features [format: bool] [default: false]")
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228 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="provide antisense features [format: bool] [default: false]")
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229 parser.add_option("-m", "--minOverlap", dest="minOverlap", action="store", default=False, type="int", help="min. #nt overlap [format: bool] [default: false]")
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230 parser.add_option("-p", "--pcOverlapQuery", dest="pcOverlapQuery", action="store", default=False, type="int", help="min. % overlap of the query [format: bool] [default: false]")
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231 parser.add_option("-P", "--pcOverlapRef", dest="pcOverlapRef", action="store", default=False, type="int", help="min. % overlap of the reference [format: bool] [default: false]")
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232 parser.add_option("-k", "--included", dest="included", action="store_true", default=False, help="provide query elements which are nested in reference elements [format: bool] [default: false]")
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233 parser.add_option("-K", "--including", dest="including", action="store_true", default=False, help="provide query elements in which reference elements are nested [format: bool] [default: false]")
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234 parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="invert the match [format: bool] [default: false]")
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235 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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236 (options, args) = parser.parse_args()
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237
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238 cosr = CompareOverlappingSmallRef(options.verbosity)
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239 cosr.setQueryFile(options.inputFileName1, options.format1)
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240 cosr.setReferenceFile(options.inputFileName2, options.format2)
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241 cosr.setOutputFile(options.outputFileName)
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242 cosr.includeNotOverlapping(options.notOverlapping)
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243 cosr.setDistance(options.distance)
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244 cosr.setAntisense(options.antisense)
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245 cosr.setInclude(options.included, options.including)
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246 cosr.setInvert(options.exclude)
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247 cosr.setMinOverlap(options.minOverlap)
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248 cosr.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef)
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249 cosr.run()
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250
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