Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
view DiffExpAnal/loadHTSeqResultFiles.py @ 6:59cc55f611f6 draft
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author | yufei-luo |
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date | Tue, 22 Jan 2013 10:46:42 -0500 |
parents | 63799b789162 |
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#!/usr/bin/env python """ Yufei LUO """ import optparse, sys def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option('-i', '--inputs', dest='inputFiles', default=None, help='several input files. (seperated by @ or @@' ) parser.add_option( '-o', '--output', dest='outputFile', default=None, help='The output list of HTSeq results files(.tabular) on txt format.' ) ( options, args ) = parser.parse_args() out = open(options.outputFile, 'w') out.write("label\tfiles\tgroup\n") if options.inputFiles == None: raise Exception, 'input file name is not defined!' groupCount = 1 fileCount = 0 inputFiles = sys.argv[6:] print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles) i = 0 while i < (len(inputFiles)-1): if inputFiles[i] == "@": i += 1 fileCount = 1 groupCount += 1 out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount)) else: fileCount += 1 out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount)) i += 1 out.close() if __name__=="__main__": __main__()