#!/usr/bin/env python
# -*- coding: utf-8

import os
import sys

import anvio
import anvio.utils as utils
import anvio.terminal as terminal
import anvio.scgsdatabase as scgsdatabase


from anvio.errors import ConfigError, FilesNPathsError




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


if __name__ == '__main__':
    import argparse
    parser = argparse.ArgumentParser(description="This programme generate pickle file with threshold\
                                                  value of assignation for each taxons by single copy core genes.")

    parser.add_argument('-s', '--scgs_directory', default = None,
                        help = "directory of single copy core genes files s")
    parser.add_argument('-t', '--taxonomy_files', default = None,
                        help = "tsv file with taxonomy")
    parser.add_argument(*anvio.A('output-file'), **anvio.K('output-file'))
    parser.add_argument(*anvio.A('num-threads'), **anvio.K('num-threads'))
    parser.add_argument('--num-process', default=2, help="num-process")

    args = anvio.get_args(parser)

    try:
        scgsdatabase = scgsdatabase.lowident(args)
        scgsdatabase.process()
    except ConfigError as e:
        print(e)
        sys.exit(-1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(-2)
