diff transform_json_to_pkl.py @ 0:abe72aa5a8b9 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transform_json_to_pkl.py	Mon Feb 20 11:26:18 2017 -0500
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import bz2
+import cPickle as pickle
+import json
+
+
+def transform_json_to_pkl(args):
+    with open(args.json_input, 'r') as json_file:
+        json_str = json_file.read()
+        metadata = json.loads(json_str)
+
+        for marker in metadata["markers"]:
+            a_set = set(metadata["markers"][marker]["ext"])
+            metadata["markers"][marker]["ext"] = a_set
+
+    pkl_output = bz2.BZ2File(args.pkl_output, 'w')
+    pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
+    pkl_output.close()
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--json_input', required=True)
+    parser.add_argument('--pkl_output', required=True)
+    args = parser.parse_args()
+
+    transform_json_to_pkl(args)