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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='outputSingleFile', default=None, help='The output list of fastq files on txt format.' )
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17 parser.add_option( '', '--pairedEnd', dest='outputPaireFile', default=None, help='paired end option help to upload the corresponding paired end complementary fastq files' )
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18 ( options, args ) = parser.parse_args()
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19
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20
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21
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22 if options.outputSingleFile == None:
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23 raise Exception, 'OutSingleFile txt file name is not defined!'
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24 else:
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25 outSingle = open(options.outputSingleFile, 'w')
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26
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27 if options.inputFiles == None:
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28 raise Exception, 'input file name is not defined!'
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29
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30 groupCount = 1
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31 fileCount = 0
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32
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33 if options.outputPaireFile == None:
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34 inputFiles = sys.argv[4:]
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35 i = 0
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36 while i < (len(inputFiles)-1):
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37 if inputFiles[i] == "@":
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38 i += 1
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39 fileCount = 1
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40 groupCount += 1
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41 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
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42
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43 else:
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44 fileCount += 1
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45 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
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46
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47 i += 1
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48 else:
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49 inputFiles = sys.argv[6:]
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50 print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles)
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51 outPaire = open(options.outputPaireFile, 'w')
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52 i = 0
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53 while i < (len(inputFiles)-1):
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54 if inputFiles[i] == "@@":
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55 i += 1
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56 outPaire.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
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57 elif inputFiles[i] == "@":
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58 i += 1
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59 fileCount = 1
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60 groupCount += 1
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61 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
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62 else:
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63 fileCount += 1
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64 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
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65
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66 i += 1
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67
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68
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69
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70 outPaire.close()
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71
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72 outSingle.close()
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73
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74
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75
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76 if __name__=="__main__": __main__()
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