Mercurial > repos > yufei-luo > s_mart

comparison SMART/DiffExpAnal/loadMultiFastqFiles.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 #!/usr/bin/env python
2
3 import optparse, sys
4
5
6 def __main__():
7 #Parse Command Line
8 parser = optparse.OptionParser()
9 parser.add_option('-i', '--inputs', dest='inputFiles', default=None, help='several input files. (seperated by @ or @@' )
10 parser.add_option( '-o', '--output', dest='outputSingleFile', default=None, help='The output list of fastq files on txt format.' )
11 parser.add_option( '', '--pairedEnd', dest='outputPaireFile', default=None, help='paired end option help to upload the corresponding paired end complementary fastq files' )
12 ( options, args ) = parser.parse_args()
13
14
15
16 if options.outputSingleFile == None:
17 raise Exception, 'OutSingleFile txt file name is not defined!'
18 else:
19 outSingle = open(options.outputSingleFile, 'w')
20
21 if options.inputFiles == None:
22 raise Exception, 'input file name is not defined!'
23
24 groupCount = 1
25 fileCount = 0
26
27 if options.outputPaireFile == None:
28 inputFiles = sys.argv[4:]
29 i = 0
30 while i < (len(inputFiles)-1):
31 if inputFiles[i] == "@":
32 i += 1
33 fileCount = 1
34 groupCount += 1
35 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
36
37 else:
38 fileCount += 1
39 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
40
41 i += 1
42 else:
43 inputFiles = sys.argv[6:]
44 print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles)
45 outPaire = open(options.outputPaireFile, 'w')
46 i = 0
47 while i < (len(inputFiles)-1):
48 if inputFiles[i] == "@@":
49 i += 1
50 outPaire.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
51 elif inputFiles[i] == "@":
52 i += 1
53 fileCount = 1
54 groupCount += 1
55 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
56 else:
57 fileCount += 1
58 outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
59
60 i += 1
61
62
63
64 outPaire.close()
65
66 outSingle.close()
67
68
69
70 if __name__=="__main__": __main__()