Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

comparison deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/loadMultiFastqFiles.py @ 10:6e573fd3c41b draft

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author yufei-luo
date Mon, 13 May 2013 10:06:30 -0400
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9:a03838a6eb54 10:6e573fd3c41b
1 #!/usr/bin/env python
2
3 """
4 Yufei LUO
5 """
6
7
8
9 import optparse, sys
10
11
12 def __main__():
13 #Parse Command Line
14 parser = optparse.OptionParser()
15 parser.add_option('-i', '--inputs', dest='inputFiles', default=None, help='several input files. (seperated by @ or @@' )
16 parser.add_option( '-o', '--output', dest='outputSingleFile', default=None, help='The output list of fastq files on txt format.' )
17 parser.add_option( '', '--pairedEnd', dest='outputPaireFile', default=None, help='paired end option help to upload the corresponding paired end complementary fastq files' )
18 ( options, args ) = parser.parse_args()
19
20
21
22 if options.outputSingleFile == None:
23 raise Exception, 'OutSingleFile txt file name is not defined!'
24 else:
25 outSingle = open(options.outputSingleFile, 'w')
26
27 if options.inputFiles == None:
28 raise Exception, 'input file name is not defined!'
29
30 groupCount = 1
31 fileCount = 0
32
33 if options.outputPaireFile == None:
34 inputFiles = sys.argv[4:]
35 i = 0
36 while i < (len(inputFiles)-1):
37 if inputFiles[i] == "@":
38 i += 1
39 fileCount = 1
40 groupCount += 1
41 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
42
43 else:
44 fileCount += 1
45 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
46
47 i += 1
48 else:
49 inputFiles = sys.argv[6:]
50 print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles)
51 outPaire = open(options.outputPaireFile, 'w')
52 i = 0
53 while i < (len(inputFiles)-1):
54 if inputFiles[i] == "@@":
55 i += 1
56 outPaire.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
57 elif inputFiles[i] == "@":
58 i += 1
59 fileCount = 1
60 groupCount += 1
61 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
62 else:
63 fileCount += 1
64 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
65
66 i += 1
67
68
69
70 outPaire.close()
71
72 outSingle.close()
73
74
75
76 if __name__=="__main__": __main__()