Mercurial > repos > iuc > merge_metaphlan_tables
diff transform_json_to_pkl.py @ 0:3b469e230e82 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
author | iuc |
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date | Sat, 04 Mar 2017 12:23:25 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transform_json_to_pkl.py Sat Mar 04 12:23:25 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)