qseq_to_fastq.py

import sys

for qseq_file in sys.argv[1:]:
    for line in open(qseq_file):
        fields = line.strip().split("\t")
        fastqid = "@%s:%s:%s:%s:%s#%s/%s" % (fields[0], fields[2], fields[3], fields[4], fields[5], fields[6], fields[7])
        seq = fields[8].replace('.', 'N')
        quality = fields[9]
        print fastqid
        print seq
        print "+"
        print quality