expand_pyronoise_output.py

from Bio import SeqIO
import sys

seq_number = 1
for rec in SeqIO.parse(open(sys.argv[1]), "fasta"):
        cols = rec.name.split("_")
        count = int(cols[3])

        for n in xrange(count):
                print ">%s_%s_%s read%s" % (cols[0], cols[1], seq_number, seq_number)
                print rec.seq.tostring()

                seq_number += 1