diff data_manager/shapeit_ref.py @ 5:f0c7cab2f547 draft

planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 1e78071ffc35990e3ea5846a6cc07e194f886cf0

--- a/data_manager/shapeit_ref.py	Thu Sep 13 14:35:09 2018 -0400
+++ b/data_manager/shapeit_ref.py	Sat Sep 15 03:20:01 2018 -0400
@@ -37,6 +37,7 @@
     parser.add_argument('path', help='Filesystem path to directory containing this reference set')
     parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files')
     parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set')
+    parser.add_argument('sample_prefix', help='Filename prefix for sample file in this reference set')
     parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
     args = parser.parse_args()
 
@@ -45,15 +46,17 @@
 
     assert_prefix_exists(args.reference_prefix, args.path, 'reference')
     assert_prefix_exists(args.map_prefix, args.path, 'map')
+    assert_prefix_exists(args.sample_prefix, args.path, 'sample')
 
-    for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix'):
+    for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix', 'sample_prefix'):
         value = getattr(args, column)
         if '\t' in value:
             exit("TAB character found in {} argument".format(column))
 
     data_manager_dict = {}
     data_table_entry = dict(value=args.key, name=args.name, path=args.path,
-                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix)
+                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix,
+                            sample_prefix=args.sample_prefix)
     _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
 
     args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')