--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_paired_reads.py	Wed Sep 25 11:29:58 2013 -0400
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+
+"""
+Split fixed length paired end reads
+"""
+
+import os, sys
+
+if __name__ == '__main__':
+    
+    infile = sys.argv[1]
+    outfile_end1 = open(sys.argv[2], 'w')
+    outfile_end2 = open(sys.argv[3], 'w')
+    
+    i = 0
+    
+    for line in file( infile ):
+        line = line.rstrip()
+        
+        if not line:
+            continue 
+        
+        end1 = ''
+        end2 = ''
+        
+        line_index = i % 4
+        
+        if line_index == 0:
+            end1 = line + '/1'
+            end2 = line + '/2'
+        
+        elif line_index == 1:
+            seq_len = len(line)/2
+            end1 = line[0:seq_len]
+            end2 = line[seq_len:]
+        
+        elif line_index == 2:
+            end1 = line + '/1'
+            end2 = line + '/2'
+        
+        else:
+            qual_len = len(line)/2
+            end1 = line[0:qual_len]
+            end2 = line[qual_len:]
+            
+        outfile_end1.write('%s\n' %(end1))
+        outfile_end2.write('%s\n' %(end2))
+        
+        i += 1
+        
+    if  i % 4 != 0  :
+        sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n")
+    outfile_end1.close()
+    outfile_end2.close()    
\ No newline at end of file