Mercurial > repos > jjohnson > gffutils

comparison create_gffdb.py @ 1:8880c2e4b2ee draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
author jjohnson
date Mon, 16 Apr 2018 18:14:30 -0400
parents 8ba71aead5bc
children
comparison
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0:8ba71aead5bc 1:8880c2e4b2ee
16 'input_gff', 16 'input_gff',
17 help="gff3 or gtf file to load") 17 help="gff3 or gtf file to load")
18 parser.add_argument( 18 parser.add_argument(
19 'gff_sqlite', 19 'gff_sqlite',
20 help="sqlite file") 20 help="sqlite file")
21 parser.add_argument(
22 '--create_introns',
23 action='store_true',
24 help='')
25 parser.add_argument(
26 '--disable_infer_transcripts',
27 action='store_true',
28 help='')
29 parser.add_argument(
30 '--disable_infer_genes',
31 action='store_true',
32 help='')
33 parser.add_argument(
34 '-v', '--verbose', action='store_true', help='Verbose')
21 args = parser.parse_args() 35 args = parser.parse_args()
22 36
23 db = gffutils.create_db(args.input_gff, args.gff_sqlite) 37 db = gffutils.create_db(
38 args.input_gff, args.gff_sqlite,
39 disable_infer_transcripts=args.disable_infer_transcripts,
40 disable_infer_genes=args.disable_infer_genes)
24 version = db.execute('SELECT version FROM meta').fetchone()[0] 41 version = db.execute('SELECT version FROM meta').fetchone()[0]
25 print('version:%s' % version,file=sys.stdout) 42 print('version:%s' % version, file=sys.stdout)
26 dialect = db.execute('SELECT dialect FROM meta').fetchone()[0] 43 dialect = db.execute('SELECT dialect FROM meta').fetchone()[0]
44 if args.create_introns:
45 db.create_introns()
27 info = json.loads(dialect) 46 info = json.loads(dialect)
28 if 'fmt' in info: 47 if 'fmt' in info:
29 print('format:%s' % info['fmt'],file=sys.stdout) 48 print('format:%s' % info['fmt'], file=sys.stdout)
30 seqids = [r[0] for r in db.execute('SELECT distinct seqid FROM features').fetchall()] 49 seqids = [r[0] for r in
31 print('seqids:%s' % ','.join(seqids),file=sys.stdout) 50 db.execute('SELECT distinct seqid FROM features').fetchall()]
51 print('seqids:%s' % ','.join(seqids), file=sys.stdout)
32 52
33 53
34 if __name__ == "__main__": 54 if __name__ == "__main__":
35 __main__() 55 __main__()