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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31
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32 """
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33 Plot the data from the data files
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34 """
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35
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36 import os, re, math
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37 from optparse import OptionParser
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38 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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39 from SMART.Java.Python.misc.RPlotter import RPlotter
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40 from SMART.Java.Python.misc.Progress import Progress
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41 from commons.core.utils.FileUtils import FileUtils
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42
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43 class Plot(object):
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44
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45 def __init__(self, verbosity):
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46 self.verbosity = verbosity
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47 self.keep = False
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48
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49 def keepTmpFiles(self, boolean):
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50 self.keep = boolean
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51
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52 def setShape(self, shape):
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53 self.shape = shape
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54
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55 def setInputFileName(self, fileName, format):
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56 self.parser = TranscriptContainer(fileName, format, self.verbosity)
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57
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58 def setXData(self, tag, default):
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59 self.x = tag
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60 self.xDefault = default
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61
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62 def setYData(self, tag, default):
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63 self.y = tag
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64 self.yDefault = default
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65
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66 def setZData(self, tag, default):
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67 self.z = tag
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68 self.zDefault = default
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69
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70 def setNbBars(self, nbBars):
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71 self.nbBars = nbBars
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72
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73 def setOutputFileName(self, fileName):
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74 self.outputFileName = fileName
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75
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76 def setRegression(self, regression):
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77 self.regression = regression
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78
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79 def setLog(self, log):
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80 self.log = log
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81
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82 def createPlotter(self):
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83 self.plotter = RPlotter(self.outputFileName, self.verbosity, self.keep)
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84 if self.shape == "barplot":
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85 self.plotter.setBarplot(True)
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86 elif self.shape == "line":
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87 pass
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88 elif self.shape == "points":
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89 self.plotter.setPoints(True)
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90 elif self.shape == "heatPoints":
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91 self.plotter.setHeatPoints(True)
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92 else:
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93 raise Exception("Do not understand shape '%s'\n" % (self.shape))
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94
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95 self.plotter.setLog(self.log)
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96 self.plotter.setRegression(self.regression)
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97
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98 def getValues(self, transcript):
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99 x = transcript.getTagValue(self.x)
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100 y = None
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101 z = None
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102 if self.y != None:
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103 y = transcript.getTagValue(self.y)
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104 if self.z != None:
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105 z = transcript.getTagValue(self.z)
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106 if x == None:
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107 if self.xDefault != None:
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108 x = self.xDefault
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109 else:
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110 raise Exception("Error! Transcript %s do not have the x-tag %s\n" % (transcript, self.x))
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111 if self.y != None:
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112 if y == None:
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113 if self.yDefault != None:
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114 y = self.yDefault
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115 else:
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116 raise Exception("Error! Transcript %s do not have the y-tag %s\n" % (transcript, self.y))
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117 if self.z != None:
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118 if z == None:
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119 if self.zDefault != None:
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120 z = self.zDefault
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121 else:
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122 raise Exception("Error! Transcript %s do not have the z-tag %s\n" % (transcript, self.z))
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123 x = float(x)
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124 if self.y != None:
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125 y = float(y)
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126 if self.z != None:
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127 z = float(z)
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128 return (x, y, z)
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129
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130 def correctPointsToBarplot(self, line):
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131 minValue = int(math.floor(min(line.keys())))
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132 maxValue = int(math.ceil(max(line.keys())))
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133 step = (maxValue - minValue) / self.nbBars
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134 values = dict([i * step + minValue, 0] for i in range(0, self.nbBars))
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135 top = (self.nbBars - 1) * step + minValue
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136 for key, value in line.iteritems():
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46
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137 newKey = min(top, int(math.floor((key - minValue) / float(maxValue - minValue) * self.nbBars)) * step + minValue)
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38
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138 values[newKey] += value
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139 return values
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140
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141 def parseFile(self):
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142 line = {}
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143 heatLine = {}
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144
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145 cpt = 1
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146 for transcript in self.parser.getIterator():
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147 x, y, z = self.getValues(transcript)
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148 name = transcript.name
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149 if name == "unnamed transcript":
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150 name = "transcript %d" % (cpt)
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151 cpt += 1
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152 if self.shape in ("points", "heatPoints"):
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153 line[name] = (x, y)
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154 if self.shape == "heatPoints":
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155 heatLine[name] = z
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156 if self.shape == "line":
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157 line[x] = y
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158 if self.shape == "barplot":
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159 line[x] = line.get(x, 0) + 1
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160 if self.shape == "barplot":
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161 line = self.correctPointsToBarplot(line)
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162 self.plotter.setXLabel(self.x)
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163 if self.y != None:
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164 self.plotter.setYLabel(self.y)
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165 else:
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166 self.plotter.setYLabel("Count")
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167 self.plotter.addLine(line)
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168 if self.shape == "heatPoints":
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169 self.plotter.addHeatLine(heatLine)
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170 self.plotter.plot()
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171
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172 def close(self):
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173 if self.regression:
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174 print self.plotter.getCorrelationData()
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175 if self.shape == "points":
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176 rho = self.plotter.getSpearmanRho()
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177 if rho == None:
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178 print "Cannot compute Spearman rho."
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179 else:
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180 print "Spearman rho: %f" % (rho)
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181
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182 def run(self):
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183 self.createPlotter()
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184 self.parseFile()
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185 self.close()
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186
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187
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188 if __name__ == "__main__":
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189
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190 # parse command line
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191 description = "Plot v1.0.2: Plot some information from a list of transcripts. [Category: Visualization]"
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192
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193 parser = OptionParser(description = description)
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194 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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195 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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196 parser.add_option("-x", "--x", dest="x", action="store", type="string", help="tag for the x value [format: string]")
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197 parser.add_option("-y", "--y", dest="y", action="store", type="string", help="tag for the y value [format: string]")
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198 parser.add_option("-z", "--z", dest="z", action="store", default=None, type="string", help="tag for the z value [format: string]")
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199 parser.add_option("-X", "--xDefault", dest="xDefault", action="store", default=None, type="float", help="value for x when tag is not present [format: float]")
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200 parser.add_option("-Y", "--yDefault", dest="yDefault", action="store", default=None, type="float", help="value for y when tag is not present [format: float]")
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201 parser.add_option("-Z", "--zDefault", dest="zDefault", action="store", default=None, type="float", help="value for z when tag is not present [format: float]")
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202 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file names [format: output file in PNG format]")
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203 parser.add_option("-s", "--shape", dest="shape", action="store", default="barplot", type="string", help="shape of the plot [format: choice (barplot, line, points, heatPoints)]")
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204 parser.add_option("-n", "--nbBars", dest="nbBars", action="store", default=2, type="int", help="number of bars in barplot [format: int]")
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205 parser.add_option("-k", "--keep", dest="keep", action="store_true", default=False, help="keep temporary files [format: bool]")
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206 parser.add_option("-r", "--regression", dest="regression", action="store_true", default=False, help="plot regression line (in 'points' format) [format: bool]")
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207 parser.add_option("-l", "--log", dest="log", action="store", default="y", type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string]")
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208 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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209 (options, args) = parser.parse_args()
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210
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211 plot = Plot(options.verbosity)
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212 plot.setInputFileName(options.inputFileName, options.format)
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213 plot.setOutputFileName(options.outputFileName)
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214 plot.setXData(options.x, options.xDefault)
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215 plot.setYData(options.y, options.yDefault)
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216 plot.setZData(options.z, options.zDefault)
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217 plot.setShape(options.shape)
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218 plot.setNbBars(options.nbBars)
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219 plot.setRegression(options.regression)
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220 plot.setLog(options.log)
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221 plot.keepTmpFiles(options.keep)
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222 plot.run()
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223
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