comparison data_manager/shapeit_ref.py @ 5:f0c7cab2f547 draft

planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 1e78071ffc35990e3ea5846a6cc07e194f886cf0
author sanbi-uwc
date Sat, 15 Sep 2018 03:20:01 -0400
parents 094bd0114876
children
comparison
equal deleted inserted replaced
4:094bd0114876 5:f0c7cab2f547
35 parser.add_argument('key', help='Short key to identify this reference set (no spaces)') 35 parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
36 parser.add_argument('name', help='Description of reference set') 36 parser.add_argument('name', help='Description of reference set')
37 parser.add_argument('path', help='Filesystem path to directory containing this reference set') 37 parser.add_argument('path', help='Filesystem path to directory containing this reference set')
38 parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files') 38 parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files')
39 parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set') 39 parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set')
40 parser.add_argument('sample_prefix', help='Filename prefix for sample file in this reference set')
40 parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to') 41 parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
41 args = parser.parse_args() 42 args = parser.parse_args()
42 43
43 if not os.path.exists(args.path): 44 if not os.path.exists(args.path):
44 exit("Unable to find specified path {}".format(args.path)) 45 exit("Unable to find specified path {}".format(args.path))
45 46
46 assert_prefix_exists(args.reference_prefix, args.path, 'reference') 47 assert_prefix_exists(args.reference_prefix, args.path, 'reference')
47 assert_prefix_exists(args.map_prefix, args.path, 'map') 48 assert_prefix_exists(args.map_prefix, args.path, 'map')
49 assert_prefix_exists(args.sample_prefix, args.path, 'sample')
48 50
49 for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix'): 51 for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix', 'sample_prefix'):
50 value = getattr(args, column) 52 value = getattr(args, column)
51 if '\t' in value: 53 if '\t' in value:
52 exit("TAB character found in {} argument".format(column)) 54 exit("TAB character found in {} argument".format(column))
53 55
54 data_manager_dict = {} 56 data_manager_dict = {}
55 data_table_entry = dict(value=args.key, name=args.name, path=args.path, 57 data_table_entry = dict(value=args.key, name=args.name, path=args.path,
56 reference_prefix=args.reference_prefix, map_prefix=args.map_prefix) 58 reference_prefix=args.reference_prefix, map_prefix=args.map_prefix,
59 sample_prefix=args.sample_prefix)
57 _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry) 60 _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
58 61
59 args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n') 62 args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')