--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_paired_end_splitter.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,33 @@
+#Dan Blankenberg
+import sys, os, shutil
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter
+
+def main():
+    #Read command line arguments
+    input_filename = sys.argv[1]
+    input_type = sys.argv[2] or 'sanger'
+    output1_filename = sys.argv[3]
+    output2_filename = sys.argv[4]
+    
+    splitter = fastqSplitter()
+    out1 = fastqWriter( open( output1_filename, 'wb' ), format = input_type )
+    out2 = fastqWriter( open( output2_filename, 'wb' ), format = input_type )
+    
+    i = None
+    skip_count = 0
+    for i, fastq_read in enumerate( fastqReader( open( input_filename, 'rb' ), format = input_type ) ):
+        read1, read2 = splitter.split( fastq_read )
+        if read1 and read2:
+            out1.write( read1 )
+            out2.write( read2 )
+        else:
+            skip_count += 1
+    out1.close()
+    out2.close()
+    if i is None:
+        print "Your file contains no valid FASTQ reads."
+    else:
+        print 'Split %s of %s reads (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
+
+if __name__ == "__main__":
+    main()