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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, os.path, random
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32 from optparse import OptionParser
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33 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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34 from commons.core.parsing.GffParser import GffParser
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35 from commons.core.writer.Gff3Writer import Gff3Writer
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36 from commons.core.writer.TranscriptWriter import TranscriptWriter
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37 from SMART.Java.Python.misc.Progress import Progress
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38 from SMART.Java.Python.misc.RPlotter import RPlotter
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39 from SMART.Java.Python.cleanGff import CleanGff
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40 from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef
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41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
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42 from SMART.Java.Python.GetUpDownStream import GetUpDownStream
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43
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44 REFERENCE = 0
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45 QUERY = 1
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46
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47 class CountLoci(object):
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48
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49 def __init__(self, verbosity = 1):
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50 self.verbosity = verbosity
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51 self.tmpFileNames = []
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52
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53 def __del__(self):
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54 for fileName in self.tmpFileNames:
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55 if os.path.exists(fileName):
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56 os.remove(fileName)
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57
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58 def setInputFile(self, fileName, format):
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59 self.inputFileName = fileName
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60 self.inputFormat = format
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61 self.parser = TranscriptContainer(fileName, format, self.verbosity-1)
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62 if self.verbosity > 0:
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63 print "%d elements in input" % (self.parser.getNbTranscripts())
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64
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65 def setReference(self, fileName):
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66 self.referenceFileName = fileName
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67
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68 def setDistance(self, distance):
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69 self.distance = distance
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70
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71 def setOutputFileName(self, fileName):
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72 self.outputFileName = fileName
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73 self.writer = Gff3Writer(fileName, self.verbosity-1)
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74 self.outputBase = "%s_%d_" % (os.path.splitext(fileName)[0], random.randint(0, 10000))
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75
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76 def _writeTmpRef(self, tags, outputFileName):
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77 cleanGff = CleanGff(self.verbosity-1)
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78 cleanGff.setInputFileName(self.referenceFileName)
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79 cleanGff.setOutputFileName(outputFileName)
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80 cleanGff.setAcceptedTypes(tags)
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81 cleanGff.run()
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82
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83 def _getReferenceFiles(self):
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84 self.referenceFiles = {"CDS": "%scds.gff3" % (self.outputBase), \
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85 "five_prime_UTR": "%sfive.gff3" % (self.outputBase), \
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86 "three_prime_UTR": "%sthree.gff3" % (self.outputBase), \
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87 "mRNA": "%smrna.gff3" % (self.outputBase), \
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46
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88 "ncRNA": "%sncRNA.gff3" % (self.outputBase), \
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89 "transposable_element_gene": "%sTE.gff3" % (self.outputBase), \
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90 "vic": "%svicinity.gff3" % (self.outputBase)}
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91 self.tmpFileNames.extend(self.referenceFiles.values())
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92 for tag, fileName in self.referenceFiles.iteritems():
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93 if tag == "ncRNA":
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94 self._writeTmpRef(["miRNA", "ncRNA", "rRNA", "snoRNA", "snRNA", "tRNA"], fileName)
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95 elif tag == "vic":
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96 continue
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97 else:
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98 self._writeTmpRef([tag], fileName)
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99
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100 def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False):
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101 co = CompareOverlappingSmallRef(self.verbosity-1)
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102 co.setQueryFile(queryFileName, queryFormat)
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103 co.setReferenceFile(referenceFileName, referenceFormat)
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104 co.setOutputFile(outputFileName)
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105 if exclusion:
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106 co.setInvert(True)
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107 co.run()
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108 return co.nbWritten
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109
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110 def _copy(self, inputFile, tag):
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111 parser = GffParser(inputFile, self.verbosity-1)
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112 for transcript in parser.getIterator():
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113 transcript.setTagValue("locus", tag)
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114 self.writer.addTranscript(transcript)
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115
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116 def _getCds(self):
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117 outputFileName = "%sin_cds.gff3" % (self.outputBase)
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118 outputNoFileName = "%sin_nocds.gff3" % (self.outputBase)
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119 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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120 nbOverlaps = self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputFileName)
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121 self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputNoFileName, True)
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122 self._copy(outputFileName, "CDS")
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123 if self.verbosity > 0:
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124 print "%d overlaps in CDS" % (nbOverlaps)
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125 return outputNoFileName
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126
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127 def _getFivePrime(self, inputFileName):
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128 outputFileName = "%sin_five.gff3" % (self.outputBase)
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129 outputNoFileName = "%sin_nofive.gff3" % (self.outputBase)
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130 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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131 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputFileName)
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132 self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputNoFileName, True)
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133 self._copy(outputFileName, "five_prime_UTR")
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134 if self.verbosity > 0:
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135 print "%d overlaps in 5' UTR" % (nbOverlaps)
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136 return outputNoFileName
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137
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138 def _getThreePrime(self, inputFileName):
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139 outputFileName = "%sin_three.gff3" % (self.outputBase)
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140 outputNoFileName = "%sin_nothree.gff3" % (self.outputBase)
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141 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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142 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputFileName)
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143 self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputNoFileName, True)
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144 self._copy(outputFileName, "three_prime_UTR")
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145 if self.verbosity > 0:
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146 print "%d overlaps in 3' UTR" % (nbOverlaps)
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147 return outputNoFileName
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148
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149 def _getNcRna(self, inputFileName):
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150 outputFileName = "%sin_ncRna.gff3" % (self.outputBase)
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151 outputNoFileName = "%sin_noNcRna.gff3" % (self.outputBase)
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152 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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153 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputFileName)
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154 self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputNoFileName, True)
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155 self._copy(outputFileName, "ncRNA")
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156 if self.verbosity > 0:
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157 print "%d overlaps in ncRNA" % (nbOverlaps)
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158 return outputNoFileName
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159
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160 def _getTe(self, inputFileName):
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161 outputFileName = "%sin_te.gff3" % (self.outputBase)
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162 outputNoFileName = "%sin_noTe.gff3" % (self.outputBase)
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163 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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164 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputFileName)
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165 self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputNoFileName, True)
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166 self._copy(outputFileName, "TE")
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167 if self.verbosity > 0:
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168 print "%d overlaps in TE" % (nbOverlaps)
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169 return outputNoFileName
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170
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171 def _getIntron(self, inputFileName):
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172 outputFileName = "%sin_intron.gff3" % (self.outputBase)
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173 outputNoFileName = "%sin_nointron.gff3" % (self.outputBase)
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174 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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175 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputFileName)
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176 self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputNoFileName, True)
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177 self._copy(outputFileName, "intron")
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178 if self.verbosity > 0:
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179 print "%d overlaps in introns" % (nbOverlaps)
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180 return outputNoFileName
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181
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182 def _getVicinity(self, inputFileName):
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183 guds = GetUpDownStream(self.verbosity-1)
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184 guds.setInputFile(self.referenceFiles["mRNA"], "gff3")
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185 guds.setOutputFile(self.referenceFiles["vic"])
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186 guds.setDistances(self.distance, self.distance)
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187 guds.run()
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188 outputFileName = "%sout_vicinity.gff3" % (self.outputBase)
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189 outputNoFileName = "%sout_novicinity.gff3" % (self.outputBase)
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190 self.tmpFileNames.extend([outputFileName, outputNoFileName])
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191 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputFileName)
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192 nbNoOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputNoFileName, True)
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193 self._copy(outputFileName, "vicinity")
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194 self._copy(outputNoFileName, "intergenic")
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195 if self.verbosity > 0:
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196 print "%d overlaps in vicinity" % (nbOverlaps)
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197 print "%d elsewhere" % (nbNoOverlaps)
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198
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199 def run(self):
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200 self._getReferenceFiles()
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201 outputFileName = self._getCds()
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202 outputFileName = self._getFivePrime(outputFileName)
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203 outputFileName = self._getThreePrime(outputFileName)
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204 outputFileName = self._getNcRna(outputFileName)
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205 outputFileName = self._getTe(outputFileName)
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206 outputFileName = self._getIntron(outputFileName)
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207 self._getVicinity(outputFileName)
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208
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209
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210
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211 if __name__ == "__main__":
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212
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213 # parse command line
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214 description = "Count Loci v1.0.0: Count input elements with respect to CDS, 5' UTR, 3' UTR, intron, downstream, upstream. [Category: Personal]"
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215
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216 parser = OptionParser(description = description)
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217 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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218 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: transcript file format]")
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219 parser.add_option("-r", "--reference", dest="reference", action="store", type="string", help="reference file [compulsory] [format: file in GFF format]")
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220 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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221 parser.add_option("-d", "--distance", dest="distance", action="store", type="int", help="distance up/down stream [compulsory] [format: output file in GFF3 format]")
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222 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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223 (options, args) = parser.parse_args()
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224
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225 cl = CountLoci(options.verbosity)
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226 cl.setInputFile(options.inputFileName, options.format)
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227 cl.setDistance(options.distance)
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228 cl.setReference(options.reference)
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229 cl.setOutputFileName(options.outputFileName)
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230 cl.run()
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