Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/utils/FileUtils.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 glob |
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34 import shutil |
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35 import sys |
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36 import re |
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37 import math |
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38 try: |
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39 import hashlib |
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40 except: |
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41 pass |
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42 |
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43 |
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44 class FileUtils( object ): |
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45 |
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46 ## Return the number of lines in the given file |
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47 # |
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48 def getNbLinesInSingleFile( fileName ): |
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49 fileHandler = open( fileName, "r" ) |
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50 lines = fileHandler.readlines() |
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51 fileHandler.close() |
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52 if (len(lines)>0 and lines[-1]== "\n"): |
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53 return (len(lines)-1) |
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54 else : |
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55 return len(lines) |
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56 |
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57 getNbLinesInSingleFile = staticmethod( getNbLinesInSingleFile ) |
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58 |
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59 ## Return the number of lines in the files in the given list |
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60 # |
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61 def getNbLinesInFileList( lFileNames ): |
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62 count = 0 |
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63 for fileName in lFileNames: |
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64 count += FileUtils.getNbLinesInSingleFile( fileName ) |
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65 return count |
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66 |
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67 getNbLinesInFileList = staticmethod( getNbLinesInFileList ) |
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68 |
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69 ## Return True if the given file exists, False otherwise |
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70 # |
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71 def isRessourceExists( fileName ): |
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72 return os.path.exists( fileName ) |
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73 |
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74 isRessourceExists = staticmethod( isRessourceExists ) |
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75 |
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76 ## Return True if the given file is empty, False otherwise |
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77 # |
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78 def isEmpty( fileName ): |
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79 return 0 == FileUtils.getNbLinesInSingleFile( fileName ) |
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80 |
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81 isEmpty = staticmethod( isEmpty ) |
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82 |
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83 ## Return True if both files are identical, False otherwise |
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84 # |
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85 def are2FilesIdentical( file1, file2 ): |
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86 tmpFile = "diff_%s_%s" % ( os.path.basename(file1), os.path.basename(file2) ) |
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87 cmd = "diff %s %s >> %s" % ( file1, file2, tmpFile ) |
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88 returnStatus = os.system( cmd ) |
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89 if returnStatus != 0: |
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90 msg = "ERROR: 'diff' returned '%i'" % ( returnStatus ) |
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91 sys.stderr.write( "%s\n" % msg ) |
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92 sys.stderr.flush() |
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93 os.remove( tmpFile ) |
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94 return False |
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95 if FileUtils.isEmpty( tmpFile ): |
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96 os.remove( tmpFile ) |
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97 return True |
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98 else: |
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99 os.remove( tmpFile ) |
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100 return False |
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101 |
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102 are2FilesIdentical = staticmethod( are2FilesIdentical ) |
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103 |
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104 ## Return a string with all the content of the files in the given list |
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105 # |
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106 def getFileContent( lFiles ): |
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107 content = "" |
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108 lFiles.sort() |
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109 for fileName in lFiles: |
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110 currentFile = open( fileName, "r" ) |
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111 content += currentFile.read() |
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112 currentFile.close() |
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113 return content |
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114 |
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115 getFileContent = staticmethod( getFileContent ) |
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116 |
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117 ## Save content of the given file after having sorted it |
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118 # |
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119 def sortFileContent( inFile, outFile="" ): |
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120 inFileHandler = open(inFile, "r" ) |
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121 lines = inFileHandler.readlines() |
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122 inFileHandler.close() |
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123 lines.sort() |
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124 if outFile == "": |
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125 outFile = inFile |
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126 outFileHandler = open( outFile, "w" ) |
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127 outFileHandler.writelines( lines ) |
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128 outFileHandler.close() |
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129 |
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130 sortFileContent = staticmethod( sortFileContent ) |
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131 |
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132 ## Add end-of-line symbol to the given file content if necessary |
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133 # |
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134 def addNewLineAtTheEndOfFileContent( fileContent ): |
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135 if not fileContent.endswith('\n') and len(fileContent) != 0: |
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136 fileContent += '\n' |
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137 return fileContent |
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138 |
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139 addNewLineAtTheEndOfFileContent = staticmethod( addNewLineAtTheEndOfFileContent ) |
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140 |
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141 ## Concatenate files in the given list |
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142 # |
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143 def catFilesFromList( lFiles, outFile, sort=True, skipHeaders = False, separator = "" ): |
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144 if sort: |
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145 lFiles.sort() |
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146 outFileHandler = open( outFile, "a" ) |
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147 isFirstFile = True |
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148 for singleFile in lFiles: |
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149 if not isFirstFile: |
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150 outFileHandler.write(separator) |
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151 isFirstFile = False |
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152 singleFileHandler = open( singleFile, "r" ) |
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153 if skipHeaders: |
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154 singleFileHandler.readline() |
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155 line = singleFileHandler.readline() |
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156 while line: |
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157 outFileHandler.write(line) |
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158 line = singleFileHandler.readline() |
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159 singleFileHandler.close() |
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160 outFileHandler.close() |
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161 |
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162 catFilesFromList = staticmethod( catFilesFromList ) |
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163 |
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164 ## Concatenate files according to the given pattern |
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165 # |
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166 def catFilesByPattern( pattern, outFile, skipHeaders = False, separator = "" ): |
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167 lFiles = glob.glob( pattern ) |
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168 FileUtils.catFilesFromList( lFiles, outFile, skipHeaders = skipHeaders, separator = separator ) |
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169 |
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170 catFilesByPattern = staticmethod( catFilesByPattern ) |
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171 |
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172 ## Remove files listed according to the given pattern |
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173 # |
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174 # @example prefix="/home/tmp/dummy*.txt" |
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175 # |
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176 def removeFilesByPattern( prefix ): |
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177 lFiles = glob.glob( prefix ) |
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178 for f in lFiles: |
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179 os.remove( f ) |
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180 |
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181 removeFilesByPattern = staticmethod( removeFilesByPattern ) |
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182 |
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183 ## Remove files listed according to the suffixes in the given list |
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184 # |
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185 def removeFilesBySuffixList( targetPath, lSuffixes ): |
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186 if targetPath[-1] == "/": |
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187 targetPath = targetPath[:-1] |
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188 for suffix in lSuffixes: |
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189 pattern = "%s/*%s" % ( targetPath, suffix ) |
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190 FileUtils.removeFilesByPattern( pattern ) |
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191 |
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192 removeFilesBySuffixList = staticmethod( removeFilesBySuffixList ) |
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193 |
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194 ## Remove repeated blanks in the given file |
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195 # |
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196 def removeRepeatedBlanks( inFile, outFile="" ): |
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197 if outFile == "": |
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198 outFile = inFile |
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199 tmpFile = "tr_%s_%s" % ( inFile, outFile ) |
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200 cmd = "tr -s ' ' < %s > %s" % ( inFile, tmpFile ) |
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201 os.system( cmd ) |
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202 os.rename( tmpFile, outFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 |
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204 removeRepeatedBlanks = staticmethod( removeRepeatedBlanks ) |
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205 |
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206 ## Remove files in the given list |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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207 # |
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208 @staticmethod |
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209 def removeFilesFromList(lFiles): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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210 for f in lFiles: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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211 os.remove(f) |
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212 |
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213 ## Remove files in the given list if exist |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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214 # |
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215 @staticmethod |
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216 def removeFilesFromListIfExist(lFiles): |
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217 for fileName in lFiles: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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218 if FileUtils.isRessourceExists(fileName): |
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219 os.remove(fileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 |
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221 ## Append the content of a file to another file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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222 # |
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223 # @param inFile string name of the input file |
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224 # @param outFile string name of the output file |
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225 # |
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226 def appendFileContent( inFile, outFile ): |
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227 outFileHandler = open( outFile, "a" ) |
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228 inFileHandler = open( inFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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229 shutil.copyfileobj( inFileHandler, outFileHandler ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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230 inFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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231 outFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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232 |
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233 appendFileContent = staticmethod( appendFileContent ) |
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234 |
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235 |
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236 ## Replace Windows end-of-line by Unix end-of-line |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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237 # |
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238 def fromWindowsToUnixEof( inFile ): |
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239 tmpFile = "%s.tmp" % ( inFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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240 shutil.copyfile( inFile, tmpFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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241 os.remove( inFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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242 tmpFileHandler = open( tmpFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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243 inFileHandler = open( inFile, "w" ) |
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244 while True: |
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245 line = tmpFileHandler.readline() |
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246 if line == "": |
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247 break |
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248 inFileHandler.write( line.replace("\r\n","\n") ) |
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249 tmpFileHandler.close() |
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250 inFileHandler.close() |
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251 os.remove( tmpFile ) |
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252 |
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253 fromWindowsToUnixEof = staticmethod( fromWindowsToUnixEof ) |
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254 |
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255 |
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256 ## Remove duplicated lines in a file |
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257 # |
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258 # @note it preserves the initial order and handles blank lines |
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259 # |
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260 def removeDuplicatedLines( inFile ): |
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261 tmpFile = "%s.tmp" % ( inFile ) |
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262 shutil.copyfile( inFile, tmpFile ) |
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263 os.remove( inFile ) |
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264 |
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265 tmpFileHandler = open( tmpFile, "r" ) |
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266 lLines = list( tmpFileHandler.read().split("\n") ) |
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267 if lLines[-1] == "": |
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268 del lLines[-1] |
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269 sLines = set( lLines ) |
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270 tmpFileHandler.close() |
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271 os.remove( tmpFile ) |
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272 |
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273 inFileHandler = open( inFile, "w" ) |
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274 for line in lLines: |
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275 if line in sLines: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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276 inFileHandler.write( "%s\n" % ( line ) ) |
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277 sLines.remove( line ) |
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278 inFileHandler.close() |
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279 |
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280 removeDuplicatedLines = staticmethod( removeDuplicatedLines ) |
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281 |
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282 |
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283 ## Write a list of lines in a given file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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284 # |
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285 def writeLineListInFile( inFile, lLines ): |
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286 inFileHandler = open( inFile, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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287 for line in lLines: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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288 inFileHandler.write( line ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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289 inFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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290 |
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291 writeLineListInFile = staticmethod( writeLineListInFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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292 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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293 |
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294 ## Give the list of absolute path of each directory in the given directory |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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295 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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296 # @param rootPath string absolute path of the given directory |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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297 # |
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298 # @return lDirPath list of absolute directory path |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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299 # |
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300 def getAbsoluteDirectoryPathList(rootPath): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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301 lDirPath = [] |
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302 lPaths = glob.glob(rootPath + "/*") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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303 for ressource in lPaths: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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304 if os.path.isdir(ressource) : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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305 lDirPath.append(ressource) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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306 return lDirPath |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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307 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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308 getAbsoluteDirectoryPathList = staticmethod(getAbsoluteDirectoryPathList) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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309 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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311 ## Get a sublist of which each element matches/doesn't match a pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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312 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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313 # @param lPath string list of paths |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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314 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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315 # @param pattern string pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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316 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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317 # @param match bool |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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318 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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319 # @return lPathMatching list of path matching pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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320 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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321 def getSubListAccordingToPattern(lPath, pattern, match = True): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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322 lPathMatching = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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323 for path in lPath: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 if match: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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325 if re.match(".*%s.*" % pattern, path): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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326 lPathMatching.append(path) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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327 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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328 if not re.match(".*%s.*" % pattern, path): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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329 lPathMatching.append(path) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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330 return lPathMatching |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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331 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 getSubListAccordingToPattern = staticmethod(getSubListAccordingToPattern) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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333 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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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 ## Give the list of file names found in the given directory |
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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 # @param dirPath string absolute path of the given directory |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 # @return lFilesInDir list of file names |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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340 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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341 def getFileNamesList( dirPath, patternFileFilter = ".*" ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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342 lFilesInDir = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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343 lPaths = glob.glob( dirPath + "/*" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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344 for ressource in lPaths: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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345 if os.path.isfile( ressource ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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346 fileName = os.path.basename( ressource ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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347 if re.match(patternFileFilter, fileName): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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348 lFilesInDir.append( fileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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349 return lFilesInDir |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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350 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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351 getFileNamesList = staticmethod( getFileNamesList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
352 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
353 ## Return the MD5 sum of a file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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354 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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355 def getMd5SecureHash( inFile ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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356 if "hashlib" in sys.modules: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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357 md5 = hashlib.md5() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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358 inFileHandler = open( inFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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359 while True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
360 line = inFileHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
361 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
362 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
363 md5.update( line ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
364 inFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
365 return md5.hexdigest() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
366 else: |
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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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367 return "" |
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368 |
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369 getMd5SecureHash = staticmethod( getMd5SecureHash ) |
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370 |
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371 ## Cat all files of a given directory |
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372 # |
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373 # @param dir string directory name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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374 # @param outFileName string output file name |
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375 # |
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376 def catFilesOfDir(dir, outFileName): |
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377 lFiles = FileUtils.getFileNamesList(dir) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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378 lFile2 = [] |
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379 for file in lFiles: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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380 lFile2.append(dir + "/" + file) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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381 FileUtils.catFilesFromList(lFile2, outFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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382 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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383 catFilesOfDir = staticmethod(catFilesOfDir) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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384 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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385 ## Return True if size file > 0 octet |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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386 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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387 # @param fileName string file name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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388 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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389 def isSizeNotNull(fileName): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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390 size = os.path.getsize(fileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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391 if size > 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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392 return True |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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393 return False |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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394 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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395 isSizeNotNull = staticmethod(isSizeNotNull) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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396 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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397 ## Split one file into N Files by lines |
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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399 # @param fileName string file name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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400 # @param N int number of files to create |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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401 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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402 @staticmethod |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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403 def splitFileIntoNFiles(fileName, N): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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404 nbLine = FileUtils.getNbLinesInSingleFile(fileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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405 nbLinesInEachFile = nbLine |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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406 if N > nbLine: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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407 N = nbLine |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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408 if N != 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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409 nbLinesInEachFile = math.ceil(float(nbLine) / N) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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410 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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411 N = 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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412 filePrefix, fileExt = os.path.splitext(os.path.basename(fileName)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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413 fileHandler = open(fileName, "r") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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414 for i in range(1,N+1): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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415 with open("%s-%s%s" %(filePrefix, i, fileExt), "w") as f: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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416 j = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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417 while j < nbLinesInEachFile: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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418 j += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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419 f.write(fileHandler.readline()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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420 fileHandler.close() |
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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 ## Split one file into files of N lines |
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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 # @param fileName string input file name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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425 # @param N int lines number per files |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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426 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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427 @staticmethod |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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428 def splitFileAccordingToLineNumber(fileName, N): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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429 filePrefix, fileExt = os.path.splitext(os.path.basename(fileName)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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430 with open(fileName) as inF: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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431 fileNb = 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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432 line = inF.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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433 if not line or N == 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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434 outFileName = "%s-%s%s" %(filePrefix, fileNb, fileExt) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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435 f = open(outFileName, "wb") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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436 shutil.copyfileobj(open(fileName, "rb"), f) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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437 f.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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438 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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439 while line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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440 outFileName = "%s-%s%s" %(filePrefix, fileNb, fileExt) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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441 with open(outFileName, "w") as outF: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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442 lineNb = 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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443 while lineNb <= N and line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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444 outF.write(line) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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445 line = inF.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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446 lineNb += 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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447 fileNb += 1 |