#!/usr/bin/env python3

import argparse
import sys

import about
import check
import shared
import tax


def parse_arguments():
    parser = argparse.ArgumentParser(
            prog='CAT add_names',
            description='Add taxonomic names to CAT or BAT output files.',
            usage='CAT add_names -i -o -t [options] [-h / --help]',
            add_help=False)
    
    required = parser.add_argument_group('Required arguments')
    shared.add_argument(required, 'input_file', True,
            help_=('Path to input file. Can be classification or ORF2LCA '
                'output file from CAT or BAT.'))
    shared.add_argument(required, 'output_file', True)
    shared.add_argument(required, 'taxonomy_folder', True)

    optional = parser.add_argument_group('Optional arguments')
    shared.add_argument(optional, 'only_official', False)
    shared.add_argument(optional, 'exclude_scores', False)
    shared.add_argument(optional, 'force', False)
    shared.add_argument(optional, 'quiet', False)
    shared.add_argument(optional, 'help', False)

    (args, extra_args) = parser.parse_known_args()

    extra_args = [arg for (i, arg) in enumerate(extra_args) if
                  (i, arg) != (0, 'add_names')]
    if len(extra_args) > 0:
        sys.exit('error: too much arguments supplied:\n{0}'.format(
            '\n'.join(extra_args)))

    # Add extra arguments.
    shared.expand_arguments(args)

    return args


def run():
    args = parse_arguments()

    message = '# CAT v{0}.'.format(about.__version__)
    shared.give_user_feedback(message, args.log_file, args.quiet,
            show_time=False)

    errors = []

    errors.append(
            check.check_input_file(args.input_file, args.log_file, args.quiet))

    if not args.force:
        errors.append(
                check.check_output_file(
                    args.output_file, args.log_file, args.quiet))

    errors.append(
            check.check_in_and_output_file(
                args.input_file, args.output_file, args.log_file, args.quiet))

    if True in errors:
        sys.exit(1)

    (taxid2parent,
            taxid2rank) = tax.import_nodes(
                    args.nodes_dmp, args.log_file, args.quiet)
    taxid2name = tax.import_names(args.names_dmp, args.log_file, args.quiet)

    message = 'Appending names...'
    shared.give_user_feedback(message, args.log_file, args.quiet)

    with open(args.input_file, 'r') as f1:
        for line in f1:
            if line.startswith('#'):
                line = line.rstrip().split('\t')

                if 'lineage' in line:
                    lineage_index = line.index('lineage')
                else:
                    message = ('{0} is not a supported classification file.'
                            ''.format(input_file))
                    shared.give_user_feedback(
                            message, args.log_file, args.quiet, error=True)

                    sys.exit(1)
                    
                try:
                    scores_index = line.index('lineage scores')
                except:
                    scores_index = None

                full_length = len(line)

                break
        else:
            message = ('{0} is not a supported classification file.'.format(
                args.input_file))
            shared.give_user_feedback(message, log_file, quiet, error=True)

            sys.exit(1)
            
    with open(args.input_file, 'r') as f1, open(args.output_file, 'w') as outf1:
        for line in f1:
            line = line.rstrip()

            if line.startswith('#'):
                if args.only_official:
                    outf1.write('{0}\tsuperkingdom\tphylum\tclass\torder\t'
                            'family\tgenus\tspecies\n'.format(line))
                else:
                    outf1.write('{0}\tfull lineage names\n'.format(line))
                    
                continue
            
            line = line.split('\t')

            if len(line) != full_length:
                # Entry does not have a full annotation.
                outf1.write('{0}\n'.format('\t'.join(line)))

                continue

            if (line[1].startswith('no taxid found') or
                    line[2].startswith('no taxid found')):
                # ORF has database hits but the accession number is not found
                # in the taxonomy files.
                outf1.write('{0}\n'.format('\t'.join(line)))

                continue
            
            lineage = line[lineage_index].split(';')

            if scores_index is not None and not args.exclude_scores:
                scores = line[scores_index].split(';')
            else:
                scores = None

            if args.only_official:
                names = tax.convert_to_official_names(
                        lineage, taxid2rank, taxid2name, scores)
            else:
                names = tax.convert_to_names(
                        lineage, taxid2rank, taxid2name, scores)

            outf1.write('{0}\t{1}\n'.format('\t'.join(line), '\t'.join(names)))

    message = 'Names written to {0}!'.format(args.output_file)
    shared.give_user_feedback(message, args.log_file, args.quiet)

    return


if __name__ == '__main__':
    sys.exit('Run \'CAT add_names\' to add taxonomic names to CAT or BAT '
            'output files.')
