--- a/create_gffdb.py	Sun Apr 08 13:26:47 2018 -0400
+++ b/create_gffdb.py	Mon Apr 16 18:14:30 2018 -0400
@@ -18,17 +18,37 @@
     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)
+    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)
+    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)
+        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__":