Re-format FASTA file.

reformat_fasta.py

#!/usr/bin/env python

import argparse
import sys
import Bio.SeqIO

def _main():
    parser = argparse.ArgumentParser(description="Re-format fasta file")
    parser.add_argument('input', default=sys.stdin, nargs='?')
    parser.add_argument('output', default=sys.stdout, nargs='?')
    options = parser.parse_args()

    for record in Bio.SeqIO.parse(options.input, 'fasta'):
        Bio.SeqIO.write(record, options.output, 'fasta')
    
    
if __name__ == '__main__':
    _main()