#!/usr/bin/env python
from termcolor import colored

from A2G.__version__ import version
from A2G.align2consensus import *

print('\nA2G version:', colored(version, None, attrs=["bold", "blink"]),
      file=sys.stderr)
print(colored('Copyright 2020', 'red', attrs=["bold"]), 'Jose Sergio Hleap\n',
      file=sys.stderr)

parser = argparse.ArgumentParser()
parser.add_argument('global_consensus', help='Sequence consensus of the '
                                             'global region, e.g. full COI')
parser.add_argument('local_consensus',
                    help='Sequence consensus of the local region, e.g. '
                         'Leray fragment')
parser.add_argument('fasta', help='fasta file with the focal sequences')
parser.add_argument('--cpus', help='number of cpus to use', default=-1,
                    type=int)
parser.add_argument('--no_write', help='return string instead of writing',
                    action='store_true', default=False)
parser.add_argument('--out_prefix', action='store', default='A2G_aln',
                    help='Prefix of outputs')
parser.add_argument('--remove_duplicates', action='store_false',
                    help='Keep or remove duplicated sequences',
                    default=True)

args = parser.parse_args()
fasta = main(**vars(args))
if fasta is not None:
    print(fasta[0], file=sys.stdout)
