|
0
|
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__()
|
