#!/usr/bin/env python
# -*- coding: utf-8
"""Get protein sequences identified during the gene calling."""

import sys
import argparse

import anvio
import anvio.dbops as dbops
import anvio.terminal as terminal

from anvio.errors import ConfigError, FilesNPathsError


__author__ = "A. Murat Eren"
__copyright__ = "Copyright 2015, The anvio Project"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"


run = terminal.Run()
progress = terminal.Progress()


def main(args):
    dbops.export_aa_sequences_from_contigs_db(args.contigs_db, args.output_file)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="Get protein sequences from a contigs database for all gene calls.")

    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db'))
    parser.add_argument(*anvio.A('output-file'), **anvio.K('output-file'))

    args = parser.parse_args() 
    
    try:
        main(args)
    except ConfigError as e:
        print(e)
        sys.exit(-1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(-1)
