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

import sys

import anvio
import anvio.terminal as terminal

from anvio.cogs import COGs
from anvio.errors import ConfigError, FilesNPathsError
from anvio.terminal import time_program


__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"
__requires__ = ['contigs-db', 'cogs-data',]
__provides__ = ['functions',]
__description__ = ("Run NCBI's COGs to associate genes in an anvi'o contigs database with functions. "
                   "COGs database was been designed as an attempt to classify proteins from completely "
                   "sequenced genomes on the basis of the orthology concept. It is no longer actively "
                   "developed, however, it is still very effective for daily needs. You may want to "
                   "consider Pfams or the eggNOG database for more comprehensive functional insights.")


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

@time_program
def main(args):
    cogs = COGs(args)
    cogs.process()


if __name__ == '__main__':
    import argparse

    try:
        cogs = COGs(argparse.Namespace())
        available_search_methods = cogs.available_search_methods
        default_search_method = cogs.default_search_method
    except ConfigError as e:
        print(e)
        sys.exit(-1)

    parser = argparse.ArgumentParser(description=__description__)

    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db'))
    parser.add_argument(*anvio.A('cog-data-dir'), **anvio.K('cog-data-dir'))
    parser.add_argument(*anvio.A('num-threads'), **anvio.K('num-threads'))
    parser.add_argument(*anvio.A('sensitive'), **anvio.K('sensitive'))
    parser.add_argument(*anvio.A('temporary-dir-path'), **anvio.K('temporary-dir-path'))

    parser.add_argument('--search-with', default=default_search_method, metavar="SEARCH_METHOD",
                        help="What program to use for database searching. The default search uses %(default)s.\
                              All available options include: %(serach_methods)s." \
                                        % {'serach_methods': ', '.join(available_search_methods),
                                           'default': default_search_method})

    args = anvio.get_args(parser)

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