ReplaceFastaLabelsFromTable

#!/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_text_iter

_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', nargs='?', type=argparse.FileType('r'),
                        default=sys.stdin,
                        help="input fasta file")
    parser.add_argument("--tsv", type=os.path.abspath,
                        help="TSV file")
    parser.add_argument("--csv", type=os.path.abspath,
                        help="CSV file")
    parser.add_argument('--out', type=os.path.abspath,
                        default=sys.stdout, help="output fasta file")
    parser.add_argument("--exact", action="store_true",
                        help="exact matching (default=inexact)")
    parser.add_argument("--colsearch", type=int, default=1,
                        help="1-based column index for search term")
    parser.add_argument("--colreplace", type=int, default=2,
                        help="1-based column index for replace term")
    parser.add_argument("--strict", action="store_true",
                        help="exit program if match not found")
    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)
    newlabels = {}
    if args.csv is not None and args.tsv is not None:
        raise RuntimeError("--tsv and --csv should not be used together")
    if args.csv is None and args.tsv is None:
        raise RuntimeError("--tsv or --csv required")
    if args.csv is not None:
        with open(args.csv) as csvfile:
            for line in csvfile:
                entry = line.rstrip().split(',')
                newlabels[entry[args.colsearch - 1]] = entry[args.colreplace - 1]
    if args.tsv is not None:
        with open(args.tsv) as tsvfile:
            for line in tsvfile:
                entry = line.rstrip().split('\t')
                newlabels[entry[args.colsearch - 1]] = entry[args.colreplace - 1]
    for hdr, seq in fasta_text_iter(args.fasta):
        newlabel = None
        if args.exact is True:
            newlabel = newlabels.get(hdr, None)
        else:
            for tag in newlabels:
                if tag in hdr:
                    newlabel = newlabels[tag]
                    break
        if newlabel is None and args.strict is True:
            raise RuntimeError("'{}' exact match not found in table".format(hdr))
        if newlabel is None and args.strict is False:
            print("'{}' exact match not found in table".format(hdr))
        print(">{}\n{}".format(newlabel, seq))
    return ''


if __name__ == '__main__':
    main()