Convert aligned reads CSV to FASTA format

aln2fasta.py

import argparse
import csv
import itertools
from operator import itemgetter

parser = argparse.ArgumentParser()
parser.add_argument('aligned',
                    type=argparse.FileType('rU'),
                    help='aligned reads CSV file')
parser.add_argument('--out',
                    '-o',
                    help='base file name for output FASTA files (if not ' +
                        'provided, a list of seeds is printed)')
args = parser.parse_args()

reader = csv.DictReader(args.aligned)
for refname, rows in itertools.groupby(reader, itemgetter('refname')):
    if not args.out:
        print refname
    else:
        filename = "{}.{}.fasta".format(args.out, refname)
        print filename
        with open(filename, 'w') as writer:
            for row in rows:
                count = int(row['count'])
                writer.write('>r{}n{}\n'.format(row['rank'], count))
                seq = ('-'*count) + (row['seq'].replace('n', '-'))
                width = 75
                for i in range(0, len(seq), width):
                    line = seq[i:i+width]
                    writer.write(line + '\n')