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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
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33 from commons.core.parsing.ParserChooser import ParserChooser
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34 from commons.core.parsing.FastaParser import FastaParser
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from commons.core.writer.Gff3Writer import Gff3Writer
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37 from SMART.Java.Python.misc.RPlotter import RPlotter
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38 from SMART.Java.Python.misc.MultipleRPlotter import MultipleRPlotter
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39 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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40 from SMART.Java.Python.misc.Progress import Progress
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41
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42 TWOSTRANDS = {True: [1, -1], False: [0]}
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43 STRANDTOSTR = {1: "(+)", -1: "(-)", 0: ""}
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44
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45 class GetDistribution(object):
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46
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47 def __init__(self, verbosity):
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46
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48 self.verbosity = verbosity
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49 self.sizes = None
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50 self.nbBins = None
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51 self.sliceSize = None
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52 self.twoStrands = False
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53 self.start = 1
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54 self.names = ["nbElements"]
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55 self.average = False
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56 self.nbValues = {}
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57 self.height = 300
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58 self.width = 600
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59 self.dots = False
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60 self.colors = None
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61 self.gffFileName = None
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62 self.csvFileName = None
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63 self.yMin = None
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64 self.yMax = None
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65 self.chromosome = None
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66 self.merge = False
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67 self.nbTranscripts = None
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68 self.factors = None
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69 self.thicknessCurve = 1
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70 self.sizePoliceLegend = 1.5
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36
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71
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46
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72 def setInputFiles(self, fileNames, format):
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73 self.fileNames = fileNames
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74 self.format = format
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36
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75
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76 def setReferenceFile(self, fileName):
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77 if fileName == None:
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78 return
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79 fastaParser = FastaParser(fileName, self.verbosity)
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80 self.chromosomes = fastaParser.getRegions()
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81 self.sizes = dict([region, fastaParser.getSizeOfRegion(region)] for region in self.chromosomes)
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82 self.maxSize = max(self.sizes.values())
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83
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84 def setRegion(self, chromosome, start, end):
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46
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85 if chromosome == None or start == None or end == None:
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86 return
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87 self.maxSize = options.end
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88 self.sizes = {chromosome: end}
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89 self.chromosomes = [chromosome]
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90 self.chromosome = chromosome
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91 self.start = start
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92 self.end = end
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93
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94 def setOutputFile(self, fileName):
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95 self.outputFileName = fileName
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96
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97 def setNbBins(self, nbBins):
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46
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98 if nbBins != None:
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99 self.nbBins = int(nbBins)
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100
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101 def setBinSize(self, binSize):
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102 if binSize != None:
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103 self.sliceSize = int(binSize)
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104
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105 def set2Strands(self, twoStrands):
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106 self.twoStrands = twoStrands
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107
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108 def setNames(self, names):
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109 self.names = names
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46
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110 if len(self.names) == 1 and len(self.fileNames) > 1:
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111 self.names = ["file %d" % (i+1) for i in range(len(self.fileNames))]
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112
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113 def setAverage(self, average):
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114 self.average = average
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115
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116 def setNormalization(self, normalization):
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117 self.normalization = normalization
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118
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46
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119 def setNormalizationFactors(self, factors):
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120 self.factors = dict([name, 1.0] for name in self.names) if factors == None else dict(zip(self.names, factors))
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121
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122 def setImageSize(self, height, width):
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123 self.height = height
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124 self.width = width
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125
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46
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126 def setDots(self, dots):
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127 self.dots = dots
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128
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129 def setYLimits(self, yMin, yMax):
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130 self.yMin = yMin
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131 self.yMax = yMax
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132
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133 def setColors(self, colors):
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134 self.colors = colors
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135
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136 def writeGff(self, fileName):
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137 self.gffFileName = fileName
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138
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139 def writeCsv(self, fileName):
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140 self.csvFileName = fileName
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141
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142 def mergePlots(self, merge):
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143 self.merge = merge
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144
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46
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145 def setThicknessCurve(self, thickness) :
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146 self.thickness = thickness
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147
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148 def setSizePoliceLegend(self, sizePoliceLegend):
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149 self.sizePoliceLegend = sizePoliceLegend
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150
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151 def _estimateSizes(self):
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46
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152 self.sizes = {}
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153 self.nbTranscripts = {}
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154 for fileName in self.fileNames:
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155 progress = UnlimitedProgress(10000, "Reading %s for chromosome size estimate" % (fileName), self.verbosity)
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156 parserChooser = ParserChooser(self.verbosity)
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157 parserChooser.findFormat(self.format)
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158 parser = parserChooser.getParser(fileName)
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159 for nbTranscripts, transcript in enumerate(parser.getIterator()):
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160 if transcript.__class__.__name__ == "Mapping":
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161 transcript = transcript.getTranscript()
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162 chromosome = transcript.getChromosome()
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163 start = transcript.getStart()
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164 self.sizes[chromosome] = max(start, self.sizes.get(chromosome, 0))
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165 progress.inc()
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166 progress.done()
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167 self.nbTranscripts[fileName] = nbTranscripts
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36
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168
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169 def _computeSliceSize(self):
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170 if self.nbBins == 0:
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171 return
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172 tmp1 = int(max(self.sizes.values()) / float(self.nbBins))
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173 tmp2 = 10 ** (len("%d" % (tmp1))-2)
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174 self.sliceSize = max(1, int((tmp1 / tmp2) * tmp2))
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175 if self.verbosity > 0:
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176 print "choosing bin size of %d" % (self.sliceSize)
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177
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178 def _initBins(self):
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179 self.bins = {}
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180 for chromosome in self.sizes:
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181 self.bins[chromosome] = {}
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182 for name in self.names:
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183 self.bins[chromosome][name] = {}
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184 for strand in TWOSTRANDS[self.twoStrands]:
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185 if self.nbBins == 0:
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186 self.bins[chromosome][name][strand] = {}
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187 else:
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188 self.bins[chromosome][name][strand] = dict([(i * self.sliceSize + 1, 0.0) for i in range(self.start / self.sliceSize, self.sizes[chromosome] / self.sliceSize + 1)])
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189
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190 def _populateBins(self):
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46
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191 for id, fileName in enumerate(self.fileNames):
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192 if self.nbTranscripts == None:
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193 progress = UnlimitedProgress(10000, "Counting data", self.verbosity)
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194 else:
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195 progress = Progress(self.nbTranscripts[fileName], "Counting data", self.verbosity)
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196 parserChooser = ParserChooser(self.verbosity)
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197 parserChooser.findFormat(self.format)
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198 parser = parserChooser.getParser(fileName)
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199 for transcript in parser.getIterator():
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200 if transcript.__class__.__name__ == "Mapping":
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201 transcript = transcript.getTranscript()
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202 progress.inc()
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203 chromosome = transcript.getChromosome()
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204 start = transcript.getStart()
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205 if self.chromosome and (chromosome != self.chromosome or start < self.start or start > self.end):
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206 continue
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207 strand = transcript.getDirection() if self.twoStrands else 0
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208 if self.nbBins != 0:
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209 bin = (start / self.sliceSize) * self.sliceSize + 1
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210 else:
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211 bin = start
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212 if len(self.fileNames) > 1:
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213 nbElements = transcript.getTagValue("nbElements") if "nbElements" in transcript.getTagNames() else 1
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214 name = self.names[id]
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215 self.bins[chromosome][name][strand][bin] = self.bins[chromosome][name][strand].get(bin, 0) + nbElements
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216 self.nbValues[name] = self.nbValues.get(name, 0) + nbElements
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217 else:
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218 for name in self.names:
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219 value = float(transcript.tags.get(name, 1))
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220 self.bins[chromosome][name][strand][bin] = self.bins[chromosome][name][strand].get(bin, 0) + value
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221 self.nbValues[name] = self.nbValues.get(name, 0) + value
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222 progress.done()
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223
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46
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224 def _normalizeFactors(self):
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225 for chromosome in self.bins:
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226 for name in self.bins[chromosome]:
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227 for strand in self.bins[chromosome][name]:
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228 for bin in self.bins[chromosome][name][strand]:
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229 self.bins[chromosome][name][strand][bin] *= self.factors[name]
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230
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231 def _normalize(self):
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232 average = float(sum(self.nbValues.values())) / len(self.nbValues.keys())
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233 self.factors = dict([name, float(average) / self.nbValues[name]] for name in self.nbValues)
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234 self._normalizeFactors()
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235
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236 def _computeAverage(self):
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237 for chromosome in self.bins:
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238 for name in self.bins[chromosome]:
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239 for strand in self.bins[chromosome][name]:
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240 for bin in self.bins[chromosome][name][strand]:
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241 self.bins[chromosome][name][strand][bin] = float(self.bins[chromosome][name][strand][bin]) / self.sliceSize
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242
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243 def _getPlotter(self, chromosome):
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244 plot = RPlotter("%s_%s.png" % (os.path.splitext(self.outputFileName)[0], chromosome), self.verbosity)
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245 plot.setImageSize(self.width, self.height)
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46
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246 plot.setLineWidth(self.thickness)
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247 plot.setSizePoliceLegend(self.sizePoliceLegend)
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248 if self.dots:
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249 plot.setPoints(True)
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250 if self.sizes[chromosome] <= 1000:
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251 unit = "nt."
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252 ratio = 1.0
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253 elif self.sizes[chromosome] <= 1000000:
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254 unit = "kb"
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255 ratio = 1000.0
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256 else:
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257 unit = "Mb"
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258 ratio = 1000000.0
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259 if self.yMin != None:
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260 plot.setMinimumY(self.yMin)
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261 if self.yMax != None:
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262 plot.setMaximumY(self.yMax)
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263 plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
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264 if len(self.names) > 1:
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265 plot.setLegend(True, True)
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266 for i, name in enumerate(self.bins[chromosome]):
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267 for strand in self.bins[chromosome][name]:
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268 #fullName = "%s %s" % (name.replace("_", " ")[:6], STRANDTOSTR[strand])
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269 fullName = name.replace("_", " ")[:6]
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270 factor = 1 if strand == 0 else strand
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271 correctedLine = dict([(key / ratio, value * factor) for key, value in self.bins[chromosome][name][strand].iteritems()])
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272 plot.addLine(correctedLine, fullName, self.colors[i] if self.colors else None)
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273 return plot
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274
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275 def _plot(self):
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276 if self.merge:
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277 multiplePlot = MultipleRPlotter(self.outputFileName, self.verbosity)
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278 multiplePlot.setImageSize(self.width, self.height * len(self.bins.keys()))
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279 progress = Progress(len(self.bins.keys()), "Plotting", options.verbosity)
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280 for chromosome in sorted(self.bins.keys()):
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281 plot = self._getPlotter(chromosome)
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282 if self.merge:
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283 multiplePlot.addPlot(plot)
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284 else:
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285 plot.plot()
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286 progress.inc()
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287 if self.merge:
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288 multiplePlot.plot()
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289 progress.done()
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290
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291 def _writeCsv(self):
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292 if self.verbosity > 1:
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293 print "Writing CSV file..."
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294 csvHandle = open(self.csvFileName, "w")
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295 csvHandle.write("chromosome;tag;strand")
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296 if self.nbBins != 0:
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297 xValues = range(self.start / self.sliceSize, max(self.sizes.values()) / self.sliceSize + 1)
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298 for value in xValues:
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299 csvHandle.write(";%d-%d" % (value * self.sliceSize + 1, (value+1) * self.sliceSize))
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300 csvHandle.write("\n")
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301 else:
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302 xValues = []
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303 for chromosome in self.bins:
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304 for name in self.bins[chromosome]:
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305 for strand in self.bins[chromosome][name]:
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306 for bin in self.bins[chromosome][name][strand]:
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307 xValues.extend(self.bins[chromosome][name][strand].keys())
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308 xValues = sorted(list(set(xValues)))
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309 for value in xValues:
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310 csvHandle.write(";%d" % (value))
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311 csvHandle.write("\n")
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312 for chromosome in self.bins:
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313 csvHandle.write("%s" % (chromosome))
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314 for name in self.bins[chromosome]:
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315 csvHandle.write(";%s" % (name))
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316 for strand in self.bins[chromosome][name]:
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317 csvHandle.write(";%s" % (STRANDTOSTR[strand]))
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318 for bin in xValues:
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319 csvHandle.write(";%.2f" % (self.bins[chromosome][name][strand].get(bin, 0)))
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320 csvHandle.write("\n")
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321 csvHandle.write(";")
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322 csvHandle.write(";")
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323 csvHandle.close()
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324 if self.verbosity > 1:
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325 print "...done"
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326
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327 def _writeGff(self):
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328 if self.verbosity > 1:
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329 print "Writing GFF file..."
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330 writer = Gff3Writer(self.gffFileName, self.verbosity)
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331 cpt = 1
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332 for chromosome in self.bins:
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333 for name in self.bins[chromosome]:
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334 for strand in self.bins[chromosome][name]:
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335 for bin in self.bins[chromosome][name][strand]:
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336 transcript = Transcript()
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337 transcript.setChromosome(chromosome)
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338 transcript.setStart(bin)
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339 if self.nbBins > 0:
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340 transcript.setEnd(bin + self.sliceSize)
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341 else:
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342 transcript.setEnd(self.start)
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343 transcript.setDirection(1 if strand == 0 else strand)
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344 transcript.setTagValue("ID", "region%d" % (cpt))
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345 cpt += 1
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346 writer.write()
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347 if self.verbosity > 1:
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348 print "...done"
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349
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350 def run(self):
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351 if self.sizes == None:
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352 self._estimateSizes()
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46
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353 if self.sliceSize == None:
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354 self._computeSliceSize()
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36
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355 self._initBins()
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356 self._populateBins()
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357 if self.normalization:
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358 self._normalize()
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46
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359 if self.factors != None:
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360 self._normalizeFactors()
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36
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361 if self.average:
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362 self._computeAverage()
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363 self._plot()
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364 if self.csvFileName != None:
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365 self._writeCsv()
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366 if self.gffFileName != None:
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367 self._writeGff()
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368
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369
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370 if __name__ == "__main__":
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371
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372 description = "Get Distribution v1.0.2: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
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373
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374 parser = OptionParser(description = description)
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46
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375 parser.add_option("-i", "--input", dest="inputFileNames", action="store", type="string", help="input files separated by commas [compulsory] [format: string]")
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376 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
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377 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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378 parser.add_option("-r", "--reference", dest="referenceFileName", action="store", default=None, type="string", help="file containing the genome [format: file in FASTA format]")
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379 parser.add_option("-b", "--nbBins", dest="nbBins", action="store", default=1000, type="int", help="number of bins [default: 1000] [format: int]")
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380 parser.add_option("-B", "--binSize", dest="binSize", action="store", default=None, type="int", help="bin size [default: None] [format: int]")
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381 parser.add_option("-2", "--bothStrands", dest="bothStrands", action="store_true", default=False, help="plot one curve per strand [format: bool] [default: false]")
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382 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="plot only a chromosome [format: string]")
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383 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="start from a given region [format: int]")
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384 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="end from a given region [format: int]")
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385 parser.add_option("-y", "--yMin", dest="yMin", action="store", default=None, type="int", help="minimum value on the y-axis to plot [format: int]")
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386 parser.add_option("-Y", "--yMax", dest="yMax", action="store", default=None, type="int", help="maximum value on the y-axis to plot [format: int]")
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387 parser.add_option("-x", "--csv", dest="csv", action="store", default=None, help="write a .csv file [format: output file in CSV format] [default: None]")
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388 parser.add_option("-g", "--gff", dest="gff", action="store", default=None, help="also write GFF3 file [format: output file in GFF format] [default: None]")
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389 parser.add_option("-H", "--height", dest="height", action="store", default=500, type="int", help="height of the graphics [format: int] [default: 300]")
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390 parser.add_option("-W", "--width", dest="width", action="store", default=800, type="int", help="width of the graphics [format: int] [default: 1000]")
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391 parser.add_option("-t", "--thickness", dest="lineThickness", action="store", default=1, type="int", help="thickness of the lines [format : int] [default : 1]")
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392 parser.add_option("-d", "--policeLegend", dest="sizePoliceLegend", action="store", default=1.5, type="float", help="size of the police of the legend [format : float] [default : 1.5]")
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393 parser.add_option("-D", "--dots", dest="dots", action="store_true", default=False, help="plot dots instead of lines [format : bool] [default : false]")
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394 parser.add_option("-a", "--average", dest="average", action="store_true", default=False, help="plot average (instead of sum) [default: false] [format: boolean]")
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395 parser.add_option("-n", "--names", dest="names", action="store", default="nbElements", type="string", help="name for the tags (separated by commas and no space) [default: None] [format: string]")
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396 parser.add_option("-l", "--color", dest="colors", action="store", default=None, type="string", help="color of the lines (separated by commas and no space) [format: string]")
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397 parser.add_option("-z", "--normalize", dest="normalize", action="store_true", default=False, help="normalize data (when panels are different) [format: bool] [default: false]")
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398 parser.add_option("-Z", "--normalizeFac", dest="normalizeFactors", action="store", default=None, help="normalize data with given factors (when panels are different) [format: string]")
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399 parser.add_option("-m", "--merge", dest="mergePlots", action="store_true", default=False, help="merge all plots in one figure [format: bool] [default: false]")
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400 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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36
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401 (options, args) = parser.parse_args()
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402
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403 gt = GetDistribution(options.verbosity)
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46
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404 gt.setInputFiles(options.inputFileNames.split(","), options.format)
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36
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405 gt.setOutputFile(options.outputFileName)
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406 gt.setReferenceFile(options.referenceFileName)
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46
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407 gt.setNbBins(options.nbBins)
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408 gt.setBinSize(options.binSize)
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36
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409 gt.set2Strands(options.bothStrands)
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410 gt.setRegion(options.chromosome, options.start, options.end)
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411 gt.setNormalization(options.normalize)
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412 gt.setAverage(options.average)
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413 gt.setYLimits(options.yMin, options.yMax)
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414 gt.writeCsv(options.csv)
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415 gt.writeGff(options.gff)
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416 gt.setImageSize(options.height, options.width)
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417 gt.setNames(options.names.split(","))
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46
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418 gt.setThicknessCurve(options.lineThickness)
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419 gt.setSizePoliceLegend(options.sizePoliceLegend)
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36
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420 gt.setColors(None if options.colors == None else options.colors.split(","))
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46
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421 gt.setDots(options.dots)
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36
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422 gt.setNormalization(options.normalize)
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46
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423 gt.setNormalizationFactors(None if options.normalizeFactors == None else [float(factor) for factor in options.normalizeFactors.split(",")])
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36
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424 gt.mergePlots(options.mergePlots)
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425 gt.run()
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426
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