Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

comparison DiffExpAnal/loadHTSeqResultFiles.py @ 0:63799b789162 draft

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author yufei-luo
date Tue, 22 Jan 2013 10:07:03 -0500
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-1:000000000000 0:63799b789162
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='outputFile', default=None, help='The output list of HTSeq results files(.tabular) on txt format.' )
17 ( options, args ) = parser.parse_args()
18
19
20 out = open(options.outputFile, 'w')
21 out.write("label\tfiles\tgroup\n")
22 if options.inputFiles == None:
23 raise Exception, 'input file name is not defined!'
24
25 groupCount = 1
26 fileCount = 0
27
28 inputFiles = sys.argv[6:]
29 print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles)
30 i = 0
31 while i < (len(inputFiles)-1):
32 if inputFiles[i] == "@":
33 i += 1
34 fileCount = 1
35 groupCount += 1
36 out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount))
37 else:
38 fileCount += 1
39 out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount))
40 i += 1
41
42 out.close()
43
44
45
46 if __name__=="__main__": __main__()