Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/GetDifferentialExpression.py @ 4:1fc014126d55
Uploaded
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:45:50 -0500 |
parents | e0f8dcca02ed |
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rev | line source |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 """Get the differential expression between 2 conditions (2 files), on regions defined by a third file""" |
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32 |
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33 import os, re |
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34 from optparse import OptionParser |
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35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer |
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36 from commons.core.writer.Gff3Writer import Gff3Writer |
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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.misc import Utils |
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40 from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection |
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41 from SMART.Java.Python.structure.Transcript import Transcript |
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42 |
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43 class GetDifferentialExpression(object): |
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44 |
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45 def __init__(self, verbosity = 1): |
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46 self.verbosity = verbosity |
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47 self.mySqlConnection = MySqlConnection(verbosity) |
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48 self.inputs = (0, 1) |
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49 self.transcriptContainers = [None, None] |
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50 self.transcriptContainerRef = None |
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51 self.outputFileName = None |
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52 self.writer = None |
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53 self.tables = [None, None] |
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54 self.nbElements = [0, 0] |
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55 |
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56 self.regionsToValues = {} |
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57 self.regionsToNames = {} |
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58 self.valuesToPvalues = {} |
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59 |
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60 self.oriented = True |
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61 self.simpleNormalization = False |
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62 self.simpleNormalizationParameters = None |
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63 self.adjustedNormalization = False |
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64 self.fixedSizeFactor = None |
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65 self.normalizationSize = None |
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66 self.normalizationFactors = [1, 1] |
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67 self.fdr = None |
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68 self.fdrPvalue = None |
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69 |
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70 self.plot = False |
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71 self.plotter = None |
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72 self.plotterName = None |
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73 self.points = {} |
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74 |
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75 |
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76 def setInputFile(self, i, fileName, fileFormat): |
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77 self.transcriptContainers[i] = TranscriptContainer(fileName, fileFormat, self.verbosity) |
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78 self.transcriptContainers[i].mySqlConnection = self.mySqlConnection |
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79 |
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80 |
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81 def setReferenceFile(self, fileName, fileFormat): |
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82 self.transcriptContainerRef = TranscriptContainer(fileName, fileFormat, self.verbosity) |
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83 self.transcriptContainerRef.mySqlConnection = self.mySqlConnection |
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84 |
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85 |
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86 def setOutputFile(self, fileName): |
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87 self.outputFileName = fileName |
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88 self.writer = Gff3Writer(fileName, self.verbosity) |
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89 |
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90 |
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91 def setOriented(self, boolean): |
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92 self.oriented = boolean |
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93 |
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94 |
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95 def setSimpleNormalization(self, boolean): |
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96 self.simpleNormalization = boolean |
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97 |
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98 |
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99 def setSimpleNormalizationParameters(self, parameters): |
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100 if parameters != None: |
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101 self.simpleNormalization = True |
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102 self.simpleNormalizationParameters = [0, 0] |
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103 for i, splittedParameter in enumerate(parameters.split(",")): |
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104 self.simpleNormalizationParameters[i] = int(splittedParameter) |
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105 |
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106 |
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107 def setAdjustedNormalization(self, boolean): |
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108 self.adjustedNormalization = boolean |
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109 |
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110 |
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111 def setFixedSizeNormalization(self, value): |
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112 self.fixedSizeFactor = value |
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113 |
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114 |
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115 def setFdr(self, fdr): |
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116 self.fdr = fdr |
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117 |
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118 |
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119 def setPlot(self, boolean): |
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120 self.plot = boolean |
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121 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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122 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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123 def setPlotterName(self, plotterName): |
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124 self.plotterName = plotterName |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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125 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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126 def setPlotter(self): |
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127 self.plot = True |
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128 self.plotter = RPlotter(self.plotterName, self.verbosity) |
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129 self.plotter.setPoints(True) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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130 self.plotter.setLog("xy") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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131 self.points = {} |
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132 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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133 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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134 def readInput(self, i): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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135 self.transcriptContainers[i].storeIntoDatabase() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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136 self.tables[i] = self.transcriptContainers[i].getTables() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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137 progress = Progress(len(self.tables[i].keys()), "Adding indices", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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138 for chromosome in self.tables[i]: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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139 if self.oriented: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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140 self.tables[i][chromosome].createIndex("iStartEndDir_%s_%d" % (chromosome, i), ("start", "end", "direction")) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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141 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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142 self.tables[i][chromosome].createIndex("iStartEnd_%s_%d" % (chromosome, i), ("start", "end")) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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143 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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144 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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145 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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146 progress = Progress(self.transcriptContainers[i].getNbTranscripts(), "Reading sample %d" % (i +1), self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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147 for chromosome in self.tables[i]: |
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148 for transcript in self.tables[i][chromosome].getIterator(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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149 self.nbElements[i] += 1 if "nbElements" not in transcript.getTagNames() else transcript.getTagValue("nbElements") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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150 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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151 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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152 if self.verbosity > 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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153 print "%d elements in sample %d" % (self.nbElements[i], i+1) |
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154 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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155 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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156 def computeSimpleNormalizationFactors(self): |
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157 nbElements = self.nbElements |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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158 if self.simpleNormalizationParameters != None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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159 print "Using provided normalization parameters: %s" % (", ".join([str(parameter) for parameter in self.simpleNormalizationParameters])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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160 nbElements = self.simpleNormalizationParameters |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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161 avgNbElements = int(float(sum(nbElements)) / len(nbElements)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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162 for i in self.inputs: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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163 self.normalizationFactors[i] = float(avgNbElements) / nbElements[i] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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164 self.nbElements[i] *= self.normalizationFactors[i] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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165 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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166 print "Normalizing to average # reads: %d" % (avgNbElements) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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167 if self.simpleNormalizationParameters != None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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168 print "# reads: %s" % (", ".join([str(nbElement) for nbElement in self.nbElements])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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169 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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170 def __del__(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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171 self.mySqlConnection.deleteDatabase() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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172 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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173 def regionToString(self, transcript): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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174 return "%s:%d-%d(%s)" % (transcript.getChromosome(), transcript.getStart(), transcript.getEnd(), "+" if transcript.getDirection() == 1 else "-") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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175 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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176 def stringToRegion(self, region): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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177 m = re.search(r"^(\S+):(\d+)-(\d+)\((\S)\)$", region) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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178 if m == None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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179 raise Exception("Internal format error: cannot parse region '%s'" % (region)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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180 transcript = Transcript() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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181 transcript.setChromosome(m.group(1)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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182 transcript.setStart(int(m.group(2))) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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183 transcript.setEnd(int(m.group(3))) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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184 transcript.setDirection(m.group(4)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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185 return transcript |
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186 |
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187 def computeMinimumSize(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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188 self.normalizationSize = 1000000000 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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189 progress = Progress(self.transcriptContainerRef.getNbTranscripts(), "Getting minimum reference size", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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190 for transcriptRef in self.transcriptContainerRef.getIterator(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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191 self.normalizationSize = min(self.normalizationSize, transcriptRef.getEnd() - transcriptRef.getStart()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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192 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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193 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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194 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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195 print "Minimum reference size: %d" % (self.normalizationSize+1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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196 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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197 def useFixedSizeNormalization(self, start, end, starts): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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198 currentNb = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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199 sum = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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200 if not starts: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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201 return 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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202 for i in range(start - self.normalizationSize, end + 1 + self.normalizationSize): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 if i not in starts: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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204 starts[i] = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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205 for i, s in starts.iteritems(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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206 if i < start: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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207 starts[start] += s |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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208 starts[i] = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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209 for i in range(start - self.normalizationSize, end + 1): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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210 currentNb += starts[i+self.normalizationSize] - starts[i] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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211 sum += currentNb |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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212 return (float(sum) / self.normalizationSize) * (self.fixedSizeFactor / (end - start + 1)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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213 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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214 def retrieveCounts(self, transcriptRef, i): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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215 if transcriptRef.getChromosome() not in self.tables[i]: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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216 return (0, 0) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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217 cumulatedCount = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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218 cumulatedNormalizedCount = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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219 for exon in transcriptRef.getExons(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 count = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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221 starts = {} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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222 command = "SELECT start, tags FROM '%s' WHERE start >= %d AND end <= %d" % (self.tables[i][exon.getChromosome()].getName(), exon.getStart(), exon.getEnd()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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223 if self.oriented: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 command += " AND direction = %d" % (exon.getDirection()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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225 query = self.mySqlConnection.executeQuery(command) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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226 for line in query.getIterator(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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227 nb = 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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228 tags = line[1].split(";") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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229 for tag in tags: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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230 key, value = tag.split("=") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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231 if key == "nbElements": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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232 nb = int(float(value)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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233 count += nb |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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234 starts[int(line[0])] = nb |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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235 normalizedCount = count if self.fixedSizeFactor == None else self.useFixedSizeNormalization(exon.getStart(), exon.getEnd(), starts) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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236 cumulatedCount += count |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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237 cumulatedNormalizedCount += normalizedCount |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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238 return (cumulatedCount, cumulatedNormalizedCount) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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239 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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240 def getAllCounts(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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241 progress = Progress(self.transcriptContainerRef.getNbTranscripts(), "Getting counts", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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242 for cpt, transcriptRef in enumerate(self.transcriptContainerRef.getIterator()): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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243 if "ID" in transcriptRef.getTagNames(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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244 self.regionsToNames[self.regionToString(transcriptRef)] = transcriptRef.getTagValue("ID") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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245 elif transcriptRef.getName() != None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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246 self.regionsToNames[self.regionToString(transcriptRef)] = transcriptRef.getName() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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247 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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248 self.regionsToNames[self.regionToString(transcriptRef)] = "region_%d" % (cpt) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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249 values = [None, None] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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250 normalizedValues = [None, None] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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251 for i in self.inputs: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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252 values[i], normalizedValues[i] = self.retrieveCounts(transcriptRef, i) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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253 normalizedValues[i] = int(self.normalizationFactors[i] * normalizedValues[i]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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254 if sum(values) != 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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255 self.regionsToValues[self.regionToString(transcriptRef)] = (normalizedValues[0], normalizedValues[1], values[0], values[1]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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256 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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257 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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258 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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259 def computeAdjustedNormalizationFactors(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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260 nbElements = len(self.regionsToValues.keys()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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261 avgValues = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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262 progress = Progress(nbElements, "Normalization step 1", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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263 for values in self.regionsToValues.values(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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264 correctedValues = [values[i] * self.normalizationFactors[i] for i in self.inputs] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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265 avgValues.append(float(sum(correctedValues)) / len(correctedValues)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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266 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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267 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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268 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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269 sortedAvgValues = sorted(avgValues) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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270 minAvgValues = sortedAvgValues[nbElements / 4] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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271 maxAvgValues = sortedAvgValues[nbElements * 3 / 4] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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272 sums = [0, 0] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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273 progress = Progress(nbElements, "Normalization step 2", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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274 for values in self.regionsToValues.values(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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275 correctedValues = [values[i] * self.normalizationFactors[i] for i in self.inputs] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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276 avgValue = float(sum(correctedValues)) / len(correctedValues) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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277 if minAvgValues <= avgValue and avgValue <= maxAvgValues: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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278 for i in self.inputs: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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279 sums[i] += values[i] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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280 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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281 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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282 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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283 avgSums = float(sum(sums)) / len(sums) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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284 for i in self.inputs: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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285 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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286 print "Normalizing sample %d: %s to" % ((i+1), self.nbElements[i]), |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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287 self.normalizationFactors[i] *= float(avgSums) / sums[i] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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288 self.nbElements[i] *= self.normalizationFactors[i] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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289 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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290 print "%s" % (int(self.nbElements[i])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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291 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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292 def getMinimumReferenceSize(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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293 self.normalizationSize = 1000000000 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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294 progress = Progress(self.transcriptContainerRef.getNbTranscripts(), "Reference element sizes", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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295 for transcriptRef in self.transcriptContainerRef.getIterator(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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296 self.normalizationSize = min(self.normalizationSize, transcriptRef.getEnd() - transcriptRef.getStart() + 1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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297 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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298 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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299 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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300 print "Minimum reference size: %d" % (self.normalizationSize) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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301 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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302 def computePvalues(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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303 normalizedValues = set() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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304 progress = Progress(len(self.regionsToValues.keys()), "Normalizing counts", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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305 for region in self.regionsToValues: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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306 values = self.regionsToValues[region] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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307 normalizedValues0 = int(round(values[0] * self.normalizationFactors[0])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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308 normalizedValues1 = int(round(values[1] * self.normalizationFactors[1])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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309 self.regionsToValues[region] = (normalizedValues0, normalizedValues1, self.regionsToValues[region][2], self.regionsToValues[region][3]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 normalizedValues.add((normalizedValues0, normalizedValues1, self.nbElements[0] - normalizedValues0, self.nbElements[1] - normalizedValues1, self.regionsToValues[region][2], self.regionsToValues[region][3])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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311 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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312 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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313 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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314 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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315 print "Computing p-values..." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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316 self.valuesToPvalues = Utils.fisherExactPValueBulk(list(normalizedValues)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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317 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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318 print "... done" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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319 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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320 def setTagValues(self, transcript, values, pValue): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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321 for tag in transcript.getTagNames(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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322 transcript.deleteTag(tag) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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323 transcript.removeExons() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 transcript.setTagValue("pValue", str(pValue)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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325 transcript.setTagValue("nbReadsCond1", str(values[0])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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326 transcript.setTagValue("nbReadsCond2", str(values[1])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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327 transcript.setTagValue("nbUnnormalizedReadsCond1", str(values[2])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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328 transcript.setTagValue("nbUnnormalizedReadsCond2", str(values[3])) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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329 if (values[0] == values[1]) or (self.fdr != None and pValue > self.fdrPvalue): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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330 transcript.setTagValue("regulation", "equal") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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331 elif values[0] < values[1]: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 transcript.setTagValue("regulation", "up") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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333 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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334 transcript.setTagValue("regulation", "down") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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335 return transcript |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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336 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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337 def computeFdr(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 pValues = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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339 nbRegions = len(self.regionsToValues.keys()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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340 progress = Progress(nbRegions, "Computing FDR", self.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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341 for values in self.regionsToValues.values(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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342 pValues.append(self.valuesToPvalues[values[0:2]]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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343 progress.inc() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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344 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
345 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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346 for i, pValue in enumerate(reversed(sorted(pValues))): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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347 if pValue <= self.fdr * (nbRegions - 1 - i) / nbRegions: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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348 self.fdrPvalue = pValue |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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349 if self.verbosity > 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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350 print "FDR: %f, k: %i, m: %d" % (pValue, nbRegions - 1 - i, nbRegions) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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351 return |
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352 |
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353 def writeDifferentialExpression(self): |
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354 if self.plot: |
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355 self.setPlotter() |
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356 |
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357 cpt = 1 |
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358 progress = Progress(len(self.regionsToValues.keys()), "Writing output", self.verbosity) |
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359 for region, values in self.regionsToValues.iteritems(): |
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360 transcript = self.stringToRegion(region) |
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361 pValue = self.valuesToPvalues[values[0:2]] |
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362 transcript.setName(self.regionsToNames[region]) |
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363 transcript = self.setTagValues(transcript, values, pValue) |
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364 self.writer.addTranscript(transcript) |
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365 cpt += 1 |
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366 |
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367 if self.plot: |
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368 self.points[region] = (values[0], values[1]) |
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369 progress.done() |
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370 self.writer.write() |
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371 self.writer.close() |
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372 |
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373 if self.plot: |
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374 self.plotter.addLine(self.points) |
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375 self.plotter.plot() |
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376 |
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377 def getDifferentialExpression(self): |
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378 for i in self.inputs: |
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379 self.readInput(i) |
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380 |
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381 if self.simpleNormalization: |
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382 self.computeSimpleNormalizationFactors() |
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383 if self.fixedSizeFactor != None: |
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384 self.computeMinimumSize() |
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385 |
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386 self.getAllCounts() |
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387 |
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388 if self.adjustedNormalization: |
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389 self.computeAdjustedNormalizationFactors() |
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390 |
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391 self.computePvalues() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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392 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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393 if self.fdr != None: |
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394 self.computeFdr() |
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395 |
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396 self.writeDifferentialExpression() |
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397 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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398 |
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399 if __name__ == "__main__": |
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400 |
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401 # parse command line |
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402 description = "Get Differential Expression v1.0.1: Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file. [Category: Data Comparison]" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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403 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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404 parser = OptionParser(description = description) |
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405 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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406 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]") |
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407 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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408 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]") |
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409 parser.add_option("-k", "--reference", dest="referenceFileName", action="store", type="string", help="reference file [compulsory] [format: file in transcript format given by -l]") |
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410 parser.add_option("-l", "--referenceFormat", dest="referenceFormat", action="store", type="string", help="format of reference file [compulsory] [format: transcript file format]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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411 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in gff3 format]") |
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412 parser.add_option("-n", "--notOriented", dest="notOriented", action="store_true", default=False, help="if the reads are not oriented [default: False] [format: bool]") |
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413 parser.add_option("-s", "--simple", dest="simple", action="store_true", default=False, help="normalize using the number of reads in each condition [format: bool]") |
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414 parser.add_option("-S", "--simpleParameters", dest="simpleParameters", action="store", default=None, type="string", help="provide the number of reads [format: bool]") |
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415 parser.add_option("-a", "--adjusted", dest="adjusted", action="store_true", default=False, help="normalize using the number of reads of 'mean' regions [format: bool]") |
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416 parser.add_option("-x", "--fixedSizeFactor", dest="fixedSizeFactor", action="store", default=None, type="int", help="give the magnification factor for the normalization using fixed size sliding windows in reference regions (leave empty for no such normalization) [format: int]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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417 parser.add_option("-d", "--fdr", dest="fdr", action="store", default=None, type="float", help="use FDR [format: float]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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418 parser.add_option("-p", "--plot", dest="plotName", action="store", default=None, type="string", help="plot cloud plot [format: output file in PNG format]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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419 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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420 (options, args) = parser.parse_args() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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421 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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422 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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423 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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424 differentialExpression = GetDifferentialExpression(options.verbosity) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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425 differentialExpression.setInputFile(0, options.inputFileName1, options.format1) |
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426 differentialExpression.setInputFile(1, options.inputFileName2, options.format2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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427 differentialExpression.setReferenceFile(options.referenceFileName, options.referenceFormat) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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428 differentialExpression.setOutputFile(options.outputFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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429 if options.plotName != None : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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430 differentialExpression.setPlotterName(options.plotName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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431 differentialExpression.setPlotter() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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432 differentialExpression.setOriented(not options.notOriented) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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433 differentialExpression.setSimpleNormalization(options.simple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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434 differentialExpression.setSimpleNormalizationParameters(options.simpleParameters) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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435 differentialExpression.setAdjustedNormalization(options.adjusted) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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436 differentialExpression.setFixedSizeNormalization(options.fixedSizeFactor) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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437 differentialExpression.setFdr(options.fdr) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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438 differentialExpression.getDifferentialExpression() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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439 differentialExpression.mySqlConnection.deleteDatabase() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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440 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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441 |