script to reindex header names

util/ufits-fastq_reindex.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+import sys
+
+#script to reindex reads containing a ';' such as ';barcodelabel=;'
+
+def fastqreindex(input):
+    from Bio.SeqIO.QualityIO import FastqGeneralIterator
+    count = 1
+    with open(input, 'rU') as fastq:
+        for title, sequence, qual in FastqGeneralIterator(fastq):
+            cols = title.split(';')
+            header = 'R_'+str(count)+';'+cols[1]+';'
+            count += 1
+            sys.stdout.write("@%s\n%s\n+\n%s\n" % (header, sequence, qual))
+
+fastqreindex(sys.argv[1])