--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/loadMultiFastqFiles.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+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='outputSingleFile', default=None, help='The output list of fastq files on txt format.' )
+    parser.add_option( '', '--pairedEnd', dest='outputPaireFile', default=None, help='paired end option help to upload the corresponding paired end complementary fastq files' )
+    ( options, args ) = parser.parse_args()
+
+    
+
+    if options.outputSingleFile == None: 
+        raise Exception, 'OutSingleFile txt file name is not defined!'
+    else:
+        outSingle = open(options.outputSingleFile, 'w')
+    
+    if options.inputFiles == None:
+        raise Exception, 'input file name is not defined!'
+    
+    groupCount = 1
+    fileCount = 0        
+    
+    if options.outputPaireFile == None:
+        inputFiles = sys.argv[4:]
+        i = 0
+        while i < (len(inputFiles)-1):
+	    if inputFiles[i] == "@":
+                i += 1
+                fileCount = 1
+                groupCount += 1
+                outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
+                
+            else:
+                fileCount += 1
+                outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
+                
+            i += 1
+    else:
+        inputFiles = sys.argv[6:]
+        print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles)
+        outPaire = open(options.outputPaireFile, 'w')
+        i = 0
+        while i < (len(inputFiles)-1):
+            if inputFiles[i] == "@@":
+                i += 1
+                outPaire.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
+            elif inputFiles[i] == "@":
+                i += 1
+                fileCount = 1
+                groupCount += 1
+                outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
+            else:
+                fileCount += 1
+                outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i]))
+                
+            i += 1
+                
+        
+        
+        outPaire.close()
+           
+    outSingle.close()   
+    
+        
+
+if __name__=="__main__": __main__()