Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/coord/AlignUtils.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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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 import os |
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33 import sys |
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34 import shutil |
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35 from commons.core.coord.Align import Align |
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36 |
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37 |
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38 ## Static methods manipulating Align instances |
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39 # |
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40 class AlignUtils( object ): |
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41 |
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42 ## Return a list with Align instances from the given file |
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43 # |
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44 # @param inFile name of a file in the Align format |
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45 # |
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46 def getAlignListFromFile( inFile ): |
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47 lAlignInstances = [] |
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48 inFileHandler = open( inFile, "r" ) |
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49 while True: |
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50 line = inFileHandler.readline() |
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51 if line == "": |
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52 break |
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53 a = Align() |
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54 a.setFromString( line ) |
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55 lAlignInstances.append( a ) |
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56 inFileHandler.close() |
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57 return lAlignInstances |
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58 |
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59 getAlignListFromFile = staticmethod( getAlignListFromFile ) |
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60 |
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61 |
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62 ## Return a list with all the scores |
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63 # |
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64 # @param lAlignInstances: list of Align instances |
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65 # |
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66 def getListOfScores( lAlignInstances ): |
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67 lScores = [] |
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68 for iAlign in lAlignInstances: |
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69 lScores.append( iAlign.score ) |
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70 return lScores |
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71 |
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72 getListOfScores = staticmethod( getListOfScores ) |
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73 |
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74 |
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75 ## Return a list with all the scores from the given file |
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76 # |
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77 # @param inFile name of a file in the Align format |
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78 # |
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79 def getScoreListFromFile(inFile): |
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80 lScores = [] |
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81 append = lScores.append |
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82 with open(inFile, "r") as inFileHandler: |
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83 line = inFileHandler.readline() |
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84 while line: |
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85 if line != "\n": |
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86 append(int(line.split('\t')[7])) |
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87 line = inFileHandler.readline() |
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88 return lScores |
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89 |
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90 getScoreListFromFile = staticmethod( getScoreListFromFile ) |
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91 |
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92 |
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93 ## for each line of a given Align file, write the coordinates on the query and the subject as two distinct lines in a Map file |
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94 # |
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95 # @param alignFile: name of the input Align file |
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96 # @param mapFile: name of the output Map file |
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97 # |
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98 def convertAlignFileIntoMapFileWithQueriesAndSubjects( alignFile, mapFile ): |
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99 alignFileHandler = open( alignFile, "r" ) |
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100 mapFileHandler = open( mapFile, "w" ) |
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101 iAlign = Align() |
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102 while True: |
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103 line = alignFileHandler.readline() |
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104 if line == "": |
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105 break |
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106 iAlign.setFromString( line ) |
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107 iMapQ, iMapS = iAlign.getMapsOfQueryAndSubject() |
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108 iMapQ.write( mapFileHandler ) |
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109 iMapS.write( mapFileHandler ) |
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110 alignFileHandler.close() |
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111 mapFileHandler.close() |
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112 |
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113 convertAlignFileIntoMapFileWithQueriesAndSubjects = staticmethod( convertAlignFileIntoMapFileWithQueriesAndSubjects ) |
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114 |
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115 |
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116 ## for each line of a given Align file, write the coordinates of the subject on the query as one line in a Map file |
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117 # |
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118 # @param alignFile: name of the input Align file |
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119 # @param mapFile: name of the output Map file |
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120 # |
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121 def convertAlignFileIntoMapFileWithSubjectsOnQueries( alignFile, mapFile ): |
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122 alignFileHandler = open( alignFile, "r" ) |
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123 mapFileHandler = open( mapFile, "w" ) |
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124 iAlign = Align() |
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125 while True: |
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126 line = alignFileHandler.readline() |
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127 if line == "": |
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128 break |
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129 iAlign.setFromString( line ) |
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130 iMapQ = iAlign.getSubjectAsMapOfQuery() |
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131 iMapQ.write( mapFileHandler ) |
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132 alignFileHandler.close() |
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133 mapFileHandler.close() |
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134 |
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135 convertAlignFileIntoMapFileWithSubjectsOnQueries = staticmethod( convertAlignFileIntoMapFileWithSubjectsOnQueries ) |
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136 |
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137 |
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138 ## return a list of Align instances sorted in decreasing order according to their score, then their length on the query and finally their initial order |
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139 # |
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140 # @param lAligns: list of Align instances |
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141 # |
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142 def getAlignListSortedByDecreasingScoreThenLength( lAligns ): |
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143 return sorted( lAligns, key=lambda iAlign: ( 1 / float(iAlign.getScore()), 1 / float(iAlign.getLengthOnQuery()) ) ) |
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144 |
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145 getAlignListSortedByDecreasingScoreThenLength = staticmethod( getAlignListSortedByDecreasingScoreThenLength ) |
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146 |
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147 |
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148 ## Convert an Align file into a Path file |
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149 # |
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150 # @param alignFile string name of the input Align file |
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151 # @param pathFile string name of the output Path file |
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152 # |
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153 def convertAlignFileIntoPathFile( alignFile, pathFile ): |
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154 alignFileHandler = open( alignFile, "r" ) |
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155 pathFileHandler = open( pathFile, "w" ) |
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156 iAlign = Align() |
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157 countAlign = 0 |
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158 while True: |
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159 line = alignFileHandler.readline() |
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160 if line == "": |
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161 break |
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162 countAlign += 1 |
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163 iAlign.setFromString( line, "\t" ) |
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164 pathFileHandler.write( "%i\t%s\n" % ( countAlign, iAlign.toString() ) ) |
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165 alignFileHandler.close() |
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166 pathFileHandler.close() |
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167 |
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168 convertAlignFileIntoPathFile = staticmethod( convertAlignFileIntoPathFile ) |
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169 |
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170 |
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171 ## Sort an Align file |
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172 # |
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173 def sortAlignFile( inFile, outFile="" ): |
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174 if outFile == "": |
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175 outFile = "%s.sort" % ( inFile ) |
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176 prg = "sort" |
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177 cmd = prg |
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178 cmd += " -k 1,1 -k 4,4 -k 2,2n -k 3,3n -k 5,5n -k 6,6n -k 8,8n" |
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179 cmd += " %s" % ( inFile ) |
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180 cmd += " > %s" % ( outFile ) |
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181 exitStatus = os.system( cmd ) |
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182 if exitStatus != 0: |
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183 msg = "ERROR: '%s' returned '%i'" % ( prg, exitStatus ) |
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184 sys.stderr.write( "%s\n" % ( msg ) ) |
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185 sys.exit( exitStatus ) |
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186 |
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187 sortAlignFile = staticmethod( sortAlignFile ) |
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188 |
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189 |
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190 ## Write Align instances contained in the given list |
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191 # |
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192 # @param lAlign a list of Align instances |
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193 # @param fileName name of the file to write the Align instances |
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194 # @param mode the open mode of the file ""w"" or ""a"" |
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195 # |
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196 def writeListInFile( lAlign, fileName, mode="w" ): |
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197 fileHandler = open( fileName, mode ) |
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198 for iAlign in lAlign: |
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199 iAlign.write( fileHandler ) |
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200 fileHandler.close() |
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201 |
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202 writeListInFile = staticmethod( writeListInFile ) |
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203 |
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204 |
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205 ## Split a list of Align instances according to the name of the query |
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206 # |
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207 # @param lInAlign list of align instances |
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208 # @return lOutAlignList list of align instances lists |
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209 # |
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210 def splitAlignListByQueryName( lInAlign ): |
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211 lSortedAlign = sorted(lInAlign, key=lambda o: o.range_query.seqname) |
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212 lOutAlignList = [] |
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213 if len(lSortedAlign) != 0 : |
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214 lAlignForCurrentQuery = [] |
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215 previousQuery = lSortedAlign[0].range_query.seqname |
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216 for align in lSortedAlign : |
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217 currentQuery = align.range_query.seqname |
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218 if previousQuery != currentQuery : |
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219 lOutAlignList.append(lAlignForCurrentQuery) |
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220 previousQuery = currentQuery |
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221 lAlignForCurrentQuery = [] |
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222 lAlignForCurrentQuery.append(align) |
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223 |
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224 lOutAlignList.append(lAlignForCurrentQuery) |
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225 |
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226 return lOutAlignList |
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227 |
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228 splitAlignListByQueryName = staticmethod( splitAlignListByQueryName ) |
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229 |
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230 |
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231 ## Create an Align file from each list of Align instances in the input list |
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232 # |
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233 # @param lAlignList list of lists with Align instances |
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234 # @param pattern string |
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235 # @param dirName string |
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236 # |
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237 def createAlignFiles( lAlignList, pattern, dirName="" ): |
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238 savedDir = os.getcwd() |
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239 nbFiles = len(lAlignList) |
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240 countFile = 1 |
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241 if dirName != "" : |
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242 try: |
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243 os.makedirs(dirName) |
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244 except: |
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245 pass |
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246 os.chdir(dirName) |
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247 |
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248 for lAlign in lAlignList: |
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249 fileName = "%s_%s.align" % (pattern, str(countFile).zfill(len(str(nbFiles)))) |
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250 AlignUtils.writeListInFile(lAlign, fileName) |
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251 countFile += 1 |
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252 os.chdir(savedDir) |
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253 |
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254 createAlignFiles = staticmethod( createAlignFiles ) |
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255 |
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256 |
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257 ## Return a list with Align instances sorted by query name, subject name, query start, query end and score |
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258 # |
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259 def sortList( lAligns ): |
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260 return sorted( lAligns, key=lambda iAlign: ( iAlign.getQueryName(), |
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261 iAlign.getSubjectName(), |
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262 iAlign.getQueryStart(), |
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263 iAlign.getQueryEnd(), |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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264 iAlign.getScore() ) ) |
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265 |
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266 sortList = staticmethod( sortList ) |
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267 |
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268 |
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269 ## Return a list after merging all overlapping Align instances |
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270 # |
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271 def mergeList( lAligns ): |
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272 lMerged = [] |
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273 |
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274 lSorted = AlignUtils.sortList( lAligns ) |
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275 |
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276 prev_count = 0 |
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277 for iAlign in lSorted: |
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278 if prev_count != len(lSorted): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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279 for i in lSorted[ prev_count + 1: ]: |
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280 if iAlign.isOverlapping( i ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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281 iAlign.merge( i ) |
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282 IsAlreadyInList = False |
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283 for newAlign in lMerged: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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284 if newAlign.isOverlapping( iAlign ): |
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285 IsAlreadyInList = True |
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286 newAlign.merge( iAlign ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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287 lMerged [ lMerged.index( newAlign ) ] = newAlign |
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288 if not IsAlreadyInList: |
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289 lMerged.append( iAlign ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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290 prev_count += 1 |
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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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292 return lMerged |
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293 |
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294 mergeList = staticmethod( mergeList ) |
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295 |
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296 |
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297 ## Merge all Align instance in a given Align file |
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298 # |
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299 def mergeFile( inFile, outFile="" ): |
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300 if outFile == "": |
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301 outFile = "%s.merged" % ( inFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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302 if os.path.exists( outFile ): |
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303 os.remove( outFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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304 |
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305 tmpFile = "%s.sorted" % ( inFile ) |
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306 AlignUtils.sortAlignFile( inFile, tmpFile ) |
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307 |
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308 tmpF = open( tmpFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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309 dQrySbj2Aligns = {} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 prevPairQrySbj = "" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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311 while True: |
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312 line = tmpF.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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313 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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314 break |
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315 iAlign = Align() |
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316 iAlign.setFromString( line ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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317 pairQrySbj = "%s_%s" % ( iAlign.getQueryName(), iAlign.getSubjectName() ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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318 if not dQrySbj2Aligns.has_key( pairQrySbj ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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319 if prevPairQrySbj != "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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320 lMerged = AlignUtils.mergeList( dQrySbj2Aligns[ prevPairQrySbj ] ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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321 AlignUtils.writeListInFile( lMerged, outFile, "a" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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322 del dQrySbj2Aligns[ prevPairQrySbj ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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323 prevPairQrySbj = pairQrySbj |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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325 prevPairQrySbj = pairQrySbj |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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326 dQrySbj2Aligns[ pairQrySbj ] = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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327 dQrySbj2Aligns[ pairQrySbj ].append( iAlign ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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328 lMerged = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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329 if len(dQrySbj2Aligns.keys()) > 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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330 lMerged = AlignUtils.mergeList( dQrySbj2Aligns[ prevPairQrySbj ] ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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331 AlignUtils.writeListInFile( lMerged, outFile, "a" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 tmpF.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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333 os.remove( tmpFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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334 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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335 mergeFile = staticmethod( mergeFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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336 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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337 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 ## Update the scores of each match in the input file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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340 # @note the new score is the length on the query times the percentage of identity |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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341 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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342 def updateScoresInFile( inFile, outFile ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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343 inHandler = open( inFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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344 outHandler = open( outFile, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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345 iAlign = Align() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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346 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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347 while True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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348 line = inHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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349 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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350 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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351 iAlign.reset() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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352 iAlign.setFromString( line, "\t" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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353 iAlign.updateScore() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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354 iAlign.write( outHandler ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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355 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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356 inHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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357 outHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
358 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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359 updateScoresInFile = staticmethod( updateScoresInFile ) |