Extract random pairs from a FASTA file and output fake FASTQ

extractpairs.py

from Bio import SeqIO
import sys
import random

rec = SeqIO.parse(open(sys.argv[1]), "fasta").next()
insert_size = int(sys.argv[2])
rec_length = len(rec)
read_length = int(sys.argv[3])
number_seqs = int(sys.argv[4])
prefix = sys.argv[5]

fh1 = open("%s_1.fastq" % (prefix,), "w")
fh2 = open("%s_2.fastq" % (prefix,), "w")

for n in xrange(0, number_seqs):
        random_pos = random.randint( 0 + insert_size, rec_length - insert_size )
        insert = rec[random_pos : random_pos + insert_size]

        fh = open("%s_1.fastq" % (prefix,))
        print >>fh1, "@read%s/1" % (n,)
        print >>fh1, str(insert[0 : read_length].seq)
        print >>fh1, "+"
        print >>fh1, "A" * read_length
        print >>fh2, "@read%s/2" % (n,)
        print >>fh2, str(insert[0-read_length :].reverse_complement().seq)
        print >>fh2, "+"
        print >>fh2, "A" * read_length