Mercurial > repos > iuc > metaphlan2krona
view transform_json_to_pkl.py @ 1:0ff3f7810262 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
author | iuc |
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date | Fri, 19 Mar 2021 09:38:23 +0000 |
parents | fdbd63e92b01 |
children |
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#!/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)