TranslateFasta

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fileencoding=utf-8

"""
TRANSLATE FASTA
James B. Pease
"""

import os
import sys
import argparse
from mixcore import fasta_iter, translate

_LICENSE = """
http://www.github.org/jbpease/mixtape
MixTAPE: Mix of Tools for Analysis in Phylogenetics and Evolution

This file is part of MixTAPE.

MixTAPE is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

MixTAPE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with MixTAPE.  If not, see <http://www.gnu.org/licenses/>.
"""


def generate_argparser():
    parser = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        epilog=_LICENSE)
    parser.add_argument('fasta', type=os.path.abspath,
                        help="input fasta file")
    parser.add_argument('--out', type=os.path.abspath,
                        default=sys.stdout, help="output fasta file")
    parser.add_argument("--dealign", action="store_true",
                        help="remove gaps prior to translation")
    parser.add_argument("--mask-stop", action="store_true",
                        help="mask-stop codon with an X")
    parser.add_argument("--remove-stop", action="store_true",
                        help="truncate stop codons")
    return parser


def main(arguments=None):
    arguments = arguments if arguments is not None else sys.argv[1:]
    parser = generate_argparser()
    args = parser.parse_args(args=arguments)
    for hdr, seq in fasta_iter(args.fasta):
        if args.dealign:
            seq = seq.replace("-", "")
        print(">{}\n{}".format(hdr, translate(seq, remove_stop=args.remove_stop, 
                                              mask_stop=args.mask_stop)))
    return ''


if __name__ == '__main__':
    main()