diff deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/loadHTSeqResultFiles.py @ 10:6e573fd3c41b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/loadHTSeqResultFiles.py	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,46 @@
+#!/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__()