diff data_manager/shapeit_ref.py @ 0:4f7004475124 draft default tip

planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/shapeit_ref.py	Tue Sep 18 00:54:49 2018 -0400
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+from __future__ import division, print_function
+import argparse
+import json
+import os
+import os.path
+
+
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
+    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
+    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('name', help='Description of reference set')
+    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()
+
+    if not os.path.exists(args.path):
+        exit("Unable to find specified path {}".format(args.path))
+
+    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', '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,
+                            sample_prefix=args.sample_prefix)
+    _add_data_table_entry(data_manager_dict, 'shapeit2_ref', data_table_entry)
+
+    args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')