diff transform_json_to_pkl.py @ 31:83f06bee818c draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty

--- a/transform_json_to_pkl.py	Thu Jun 16 06:07:23 2016 -0400
+++ b/transform_json_to_pkl.py	Tue Feb 21 12:29:37 2017 -0500
@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import cPickle as pickle
+import argparse
 import bz2
+import cPickle as pickle
 import json
-import argparse
+
 
 def transform_json_to_pkl(args):
     with open(args.json_input, 'r') as json_file:
@@ -12,17 +13,18 @@
         metadata = json.loads(json_str)
 
         for marker in metadata["markers"]:
-            metadata["markers"][marker]["ext"] = set(metadata["markers"][marker]["ext"])
+            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)