Split FASTA file to individual entries

split-fasta.py

#!/usr/bin/env python

import Bio.SeqIO
import argparse
import re
import os.path

def cleanup_text(name):
    """
    
    Arguments:
    - `name`:
    """

    return re.sub(r'[^0-9a-zA-Z\s\-]', '_', name)


def _main():
    parser = argparse.ArgumentParser(description='Split')
    parser.add_argument('input', help='input fasta')
    parser.add_argument('output', help='Output directory')
    options = parser.parse_args()

    for record in Bio.SeqIO.parse(options.input, 'fasta'):
        with file(os.path.join(options.output, record.id+'.fa'), 'w') as f:
            Bio.SeqIO.write([record], f, 'fasta')


if __name__ == '__main__':
    _main()