Convert fasta+qual to fastq. Writes to standard out so you can pipe or use >

fastaqual_too_fastq.py

#!/usr/bin/env python

import sys

from Bio import SeqIO
from Bio.SeqIO.QualityIO import PairedFastaQualIterator

import argparse

parser = argparse.ArgumentParser()
parser.add_argument('fasta', help='Fasta file')
parser.add_argument('qual', help='Qual file')
args = parser.parse_args()

records = PairedFastaQualIterator(
    open(args.fasta),
    open(args.qual)
)
for rec in records:
    sys.stdout.write(rec.format('fastq'))