#!/opt/conda/conda-bld/mikado_1612896062182/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/python

import sys, argparse, os
# from Bio import SeqIO
from io import IOBase
import pyfaidx
import textwrap

def main():

    def check_type(string):
        if os.path.exists(string) and not os.path.isdir(string): return open(string)
        else: return set(string.split(','))

    parser=argparse.ArgumentParser(description='A simple script that retrieves the FASTA sequences from a file given a list of ids.')
    parser.add_argument("-v", "--reverse", action="store_true", default=False, help="Retrieve entries which are not in the list, as in grep -v (a homage).")
    parser.add_argument('list', type=check_type, help='File with the list of the ids to recover, one by line. Alternatively, names separated by commas.')
    parser.add_argument('fasta', type=argparse.FileType('r'), help='FASTA file.')
    parser.add_argument('out', type=argparse.FileType('w'), help='Optional output file.', nargs='?', default=sys.stdout)
    args=parser.parse_args()

    if isinstance(args.list, IOBase):
        ids = set([line.rstrip() for line in args.list.readlines()])
    else:
        ids=args.list

    args.fasta.close()
    fasta = pyfaidx.Fasta(args.fasta.name)

    for name in ids:
        assert name in fasta
        print(">{0}".format(name), file=args.out)
        print(*textwrap.wrap(str(fasta[name]), width=60),
              sep="\n", file=args.out)
        
    # for record in SeqIO.parse(args.fasta, 'fasta'):
    #     if record.id in ids:
    #         if args.reverse: continue
    #         print(record.format('fasta'), file=args.out, end='')
    #         ids.remove(record.id)
    #         if len(ids)==0 and not args.reverse: break
    #     else:
    #         if args.reverse:
    #             print(record.format('fasta'), file=args.out, end='')

if __name__=='__main__': main()
