Illumina hiseq 2000 sequencers add an extra base "A" at the end of each QSEQ read

add_final_a_index.py

#!/usr/bin/env python

import csv
import sys
import os

ss_reader = csv.DictReader(open(sys.argv[1], 'rU'))
ss_writer = csv.DictWriter(open(os.path.splitext(sys.argv[1])[0]+"_a.csv", 'w'), ss_reader.fieldnames)

ss_writer.writerow(dict((fn,fn) for fn in ss_reader.fieldnames))

for row in ss_reader:
    if len(row['Index']) < 7:
        row['Index'] = row['Index'] + "A"
        ss_writer.writerow(row)