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1 #!/usr/bin/env python
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2
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3 """
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4 Yufei LUO
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5 """
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6
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7
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8
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9 import optparse, sys
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10
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11
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12 def __main__():
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13 #Parse Command Line
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14 parser = optparse.OptionParser()
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15 parser.add_option('-i', '--inputs', dest='inputFiles', default=None, help='several input files. (seperated by @ or @@' )
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16 parser.add_option( '-o', '--output', dest='outputFile', default=None, help='The output list of HTSeq results files(.tabular) on txt format.' )
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17 ( options, args ) = parser.parse_args()
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18
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19
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20 out = open(options.outputFile, 'w')
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21 out.write("label\tfiles\tgroup\n")
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22 if options.inputFiles == None:
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23 raise Exception, 'input file name is not defined!'
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24
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25 groupCount = 1
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26 fileCount = 0
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27
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28 inputFiles = sys.argv[6:]
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29 print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles)
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30 i = 0
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31 while i < (len(inputFiles)-1):
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32 if inputFiles[i] == "@":
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33 i += 1
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34 fileCount = 1
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35 groupCount += 1
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36 out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount))
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37 else:
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38 fileCount += 1
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39 out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount))
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40 i += 1
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41
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42 out.close()
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43
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44
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45
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46 if __name__=="__main__": __main__()
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