#!/usr/bin/env python

from __future__ import print_function

import argparse
import json
import sys

import gffutils


def __main__():
    parser = argparse.ArgumentParser(
        description='Convert mga output to bed and tsv')
    parser.add_argument(
        'input_gff',
        help="gff3 or gtf file to load")
    parser.add_argument(
        'gff_sqlite',
        help="sqlite file")
    parser.add_argument(
        '--create_introns',
        action='store_true',
        help='')
    parser.add_argument(
        '--disable_infer_transcripts',
        action='store_true',
        help='')
    parser.add_argument(
        '--disable_infer_genes',
        action='store_true',
        help='')
    parser.add_argument(
        '-v', '--verbose', action='store_true', help='Verbose')
    args = parser.parse_args()

    db = gffutils.create_db(
        args.input_gff, args.gff_sqlite,
        disable_infer_transcripts=args.disable_infer_transcripts,
        disable_infer_genes=args.disable_infer_genes)
    version = db.execute('SELECT version FROM meta').fetchone()[0]
    print('version:%s' % version, file=sys.stdout)
    dialect = db.execute('SELECT dialect FROM meta').fetchone()[0]
    if args.create_introns:
        db.create_introns()
    info = json.loads(dialect)
    if 'fmt' in info:
        print('format:%s' % info['fmt'], file=sys.stdout)
    seqids = [r[0] for r in
              db.execute('SELECT distinct seqid  FROM features').fetchall()]
    print('seqids:%s' % ','.join(seqids), file=sys.stdout)


if __name__ == "__main__":
    __main__()