#!/opt/anaconda1anaconda2anaconda3/bin/python
# -*- coding: utf-8

import os
import sys

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

with terminal.SuppressAllOutput():
    import anvio.data.hmm as hmm_data

available_hmm_sources =  list(hmm_data.sources.keys())

from anvio.errors import ConfigError, FilesNPathsError
from anvio.tables.hmmhits import TablesForHMMHits


__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__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):
    # first check whether this computer is capable of doing an HMM search.
    missing_programs =  utils.get_missing_programs_for_hmm_analysis()
    if missing_programs:
        raise ConfigError("Well, in order to run this program, you need %s to be installed on your system." %\
                                                                                     (', and '.join(missing_programs)))

    # then check whether we are going to use the default HMM profiles, or run it for a new one.
    sources = {}
    if args.hmm_profile_dir and args.installed_hmm_profile:
        raise ConfigError("You must select either an installed HMM profile, or provide a path for a profile directory.\
                           But not both :/")
    elif args.hmm_profile_dir:
        if not os.path.exists(args.hmm_profile_dir):
            raise ConfigError('No such file or directory: "%s"' % args.hmm_profile_dir)
        sources = utils.get_HMM_sources_dictionary([args.hmm_profile_dir])
        run.info('HMM profiles', '%d source%s been loaded: %s' % (len(sources),
                                                          's' if len(sources) > 1 else '',
                                                          ', '.join(['%s (%d genes)' % (s, len(sources[s]['genes']))\
                                                                                                    for s in sources])))
    elif args.installed_hmm_profile:
        if args.installed_hmm_profile not in available_hmm_sources:
            raise ConfigError("You managed to find a profile that is not actually installed :/ Available ones are\
                               these: %s." % (', '.join(available_hmm_sources)))

        sources = {args.installed_hmm_profile: hmm_data.sources[args.installed_hmm_profile]}
    else:
        # sources will be loaded from defaults.
        pass

    search_tables = TablesForHMMHits(args.contigs_db, num_threads_to_use = args.num_threads)
    search_tables.populate_search_tables(sources)


if __name__ == '__main__':
    import argparse
    parser = argparse.ArgumentParser(description="This program deals with populating tables that store HMM hits in an\
                                                  anvi'o contigs database.")

    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db'))
    parser.add_argument(*anvio.A('hmm-profile-dir'), **anvio.K('hmm-profile-dir'))
    parser.add_argument(*anvio.A('installed-hmm-profile'), **anvio.K('installed-hmm-profile', {'help': "When you run this\
                                  program without any parameter, it runs all %d HMM profiles installed on your system. If\
                                  you want only a specific one to run, you can select it by using this parameter. These\
                                  are the currently available ones: %s." % \
                                                (len(available_hmm_sources),
                                                 ', '.join(['"%s" (type: %s)' % (s, hmm_data.sources[s]['kind']) \
                                                                                    for s in available_hmm_sources]))}))
    parser.add_argument(*anvio.A('num-threads'), **anvio.K('num-threads'))

    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(-2)
