diff data_manager/shapeit_ref.py @ 1:52f0767fe68d draft

planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8

--- a/data_manager/shapeit_ref.py	Tue Sep 11 10:39:38 2018 -0400
+++ b/data_manager/shapeit_ref.py	Thu Sep 13 06:25:32 2018 -0400
@@ -14,34 +14,46 @@
     return data_manager_dict
 
 
+_add_data_table_entry.__annotations__ = {'data_manager': dict, 'data_table_name': str, 'data_table_entry': dict, 'return': dict}
+
+
+def assert_prefix_exists(prefix, path, prefix_type):
+    prefix_exists = False
+    for filename in os.listdir(path):
+        if filename.startswith(prefix):
+            prefix_exists = True
+            break
+    else:
+        if not prefix_exists:
+            exit("Unable to find a file with {} prefix {} in {}".format(prefix_type, prefix, path))
+
+
+assert_prefix_exists.__annotations__ = {'prefix': str, 'path': str, 'prefix_type': str, 'return': None}
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data')
     parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
     parser.add_argument('description', help='Description of reference set')
     parser.add_argument('path', help='Filesystem path to directory containing this reference set')
-    parser.add_argument('prefix', help='Filename prefix for files in 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('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
     args = parser.parse_args()
 
     if not os.path.exists(args.path):
         exit("Unable to find specified path {}".format(args.path))
 
-    prefix_exists = False
-    for filename in os.listdir(args.path):
-        if filename.startswith(args.prefix):
-            prefix_exists = True
-            break
-    else:
-        if not prefix_exists:
-            exit("Unable to find a file with prefix {} in {}".format(args.prefix, args.path))
+    assert_prefix_exists(args.reference_prefix, args.path, 'reference')
+    assert_prefix_exists(args.map_prefix, args.path, 'map')
 
-    for column in ('key', 'description', 'path', 'prefix'):
+    for column in ('key', 'description', 'path', 'reference_prefix', 'map_prefix'):
         value = getattr(args, column)
         if '\t' in value:
             exit("TAB character found in {} argument".format(column))
 
     data_manager_dict = {}
-    data_table_entry = dict(key=args.key, description=args.description, path=args.path, prefix=args.prefix)
+    data_table_entry = dict(key=args.key, description=args.description, path=args.path,
+                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix)
     _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
 
-    args.output_file.write(json.dumps(data_manager_dict) + '\n')
+    args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')