--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_paired_end_interlacer.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,59 @@
+#Florent Angly
+import sys
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
+
+def main():
+    mate1_filename   = sys.argv[1]
+    mate1_type       = sys.argv[2] or 'sanger'
+    mate2_filename   = sys.argv[3]
+    mate2_type       = sys.argv[4] or 'sanger'
+    outfile_pairs    = sys.argv[5]
+    outfile_singles = sys.argv[6]
+
+    if mate1_type != mate2_type:
+        print "WARNING: You are trying to interlace files of two different types: %s and %s." % ( mate1_type, mate2_type )
+        return
+
+    type = mate1_type
+    joiner = fastqJoiner( type )
+    out_pairs = fastqWriter( open( outfile_pairs, 'wb' ), format = type )
+    out_singles = fastqWriter( open( outfile_singles, 'wb' ), format = type )
+
+    # Pairs + singles present in mate1
+    nof_singles = 0
+    nof_pairs   = 0
+    mate2_input = fastqNamedReader( open( mate2_filename, 'rb' ), format = type )
+    i = None
+    for i, mate1 in enumerate( fastqReader( open( mate1_filename, 'rb' ), format = type ) ):
+        mate2 = mate2_input.get( joiner.get_paired_identifier( mate1 ) )
+        if mate2:
+            out_pairs.write( mate1 )
+            out_pairs.write( mate2 )
+            nof_pairs += 1
+        else:
+            out_singles.write( mate1 )
+            nof_singles += 1
+
+    # Singles present in mate2
+    mate1_input = fastqNamedReader( open( mate1_filename, 'rb' ), format = type )
+    j = None
+    for j, mate2 in enumerate( fastqReader( open( mate2_filename, 'rb' ), format = type ) ):
+        mate1 = mate1_input.get( joiner.get_paired_identifier( mate2 ) )
+        if not mate1:
+            out_singles.write( mate2 )
+            nof_singles += 1
+
+    if (i is None) and (j is None):
+        print "Your input files contained no valid FASTQ sequences."
+    else:
+        print 'There were %s single reads.' % ( nof_singles )
+        print 'Interlaced %s pairs of sequences.' % ( nof_pairs )
+
+    mate1_input.close()
+    mate2_input.close()
+    out_pairs.close()
+    out_singles.close()
+
+ 
+if __name__ == "__main__":
+    main()