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

import os
import sys

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


from anvio.errors import ConfigError, FilesNPathsError


__author__ = "A. Murat Eren"
__copyright__ = "Copyright 2016, 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):
    # 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:
        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])))
    else:
        # sources will be loaded from defaults. 
        pass

    search_tables = dbops.TablesForHMMHits(args.contigs_db, num_threads_to_use = args.num_threads)
    search_tables.debug = args.debug
    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('num-threads'), **anvio.K('num-threads'))
    parser.add_argument(*anvio.A('debug'), **anvio.K('debug'))

    args = parser.parse_args()

    try:
        main(args)
    except ConfigError as e:
        print(e)
        sys.exit(-1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(-2)
