changeset 8:63d5d3560e51 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_table.py	Fri Jul 05 08:50:59 2019 -0400
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import os.path
+import sys
+
+def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name):
+    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('ganon_databases', [])
+    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
+    return data_manager_dict
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Download RefSeq rRNA bacterial databases')
+    parser.add_argument('--output_directory', default='/tool-data/ganon', help='Directory to write output')
+    parser.add_argument('--rrna', help='rRNA sequences to download (5S, 16S, or 23S)')
+    args = parser.parse_args()
+
+    output_directory = args.output_directory
+    if not os.path.exists(output_directory):
+        os.mkdir(output_directory)
+
+    data_manager_dict = {}
+    _add_data_table_entry(data_manager_dict=data_manager_dict,
+      data_table_entry=dict(value="ganon"+args.rrna, dbkey="gannon"+args.rrna, name=args.rrna, path=args.output_directory),
+      data_table_name='ganon_databases')
+    open("output_file", 'w').write(json.dumps(data_manager_dict, sort_keys=True))
+