--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_paired_end_deinterlacer.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,64 @@
+#Florent Angly
+import sys
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
+
+def main():
+    input_filename   = sys.argv[1]
+    input_type       = sys.argv[2] or 'sanger'
+    mate1_filename   = sys.argv[3]
+    mate2_filename   = sys.argv[4]
+    single1_filename = sys.argv[5]
+    single2_filename = sys.argv[6]
+
+    type        = input_type
+    input       = fastqNamedReader( open( input_filename, 'rb' ), format = type  )
+    mate1_out   = fastqWriter( open( mate1_filename, 'wb' ), format = type )
+    mate2_out   = fastqWriter( open( mate2_filename, 'wb' ), format = type )
+    single1_out = fastqWriter( open( single1_filename, 'wb' ), format = type )
+    single2_out = fastqWriter( open( single2_filename, 'wb' ), format = type )
+    joiner      = fastqJoiner( type )
+
+    i = None
+    skip_count = 0
+    found = {}
+    for i, mate1 in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ):
+     
+        if mate1.identifier in found:
+            del found[mate1.identifier]
+            continue
+
+        mate2 = input.get( joiner.get_paired_identifier( mate1 ) )
+
+        if mate2:
+            # This is a mate pair
+            found[mate2.identifier] = None
+            if joiner.is_first_mate( mate1 ):
+                mate1_out.write( mate1 )
+                mate2_out.write( mate2 )
+            else:
+                mate1_out.write( mate2 )
+                mate2_out.write( mate1 )
+        else:
+            # This is a single
+            skip_count += 1
+            if joiner.is_first_mate( mate1 ):
+                single1_out.write( mate1 )
+            else:
+                single2_out.write( mate1 )
+
+    if i is None:
+        print "Your input file contained no valid FASTQ sequences."
+    else:
+        if skip_count:
+            print 'There were %i reads with no mate.' % skip_count
+        print 'De-interlaced %s pairs of sequences.' % ( (i - skip_count + 1)/2 )
+
+    input.close()
+    mate1_out.close()
+    mate2_out.close()
+    single1_out.close()
+    single2_out.close()
+
+ 
+if __name__ == "__main__":
+    main()