Mercurial > repos > iuc > humann2_unpack_pathways
comparison transform_json_to_pkl.py @ 0:d2e4fee96dd1 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
| author | iuc |
|---|---|
| date | Tue, 01 Aug 2017 07:56:57 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:d2e4fee96dd1 |
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| 1 #!/usr/bin/env python | |
| 2 # -*- coding: utf-8 -*- | |
| 3 | |
| 4 import argparse | |
| 5 import bz2 | |
| 6 import cPickle as pickle | |
| 7 import json | |
| 8 | |
| 9 | |
| 10 def transform_json_to_pkl(args): | |
| 11 with open(args.json_input, 'r') as json_file: | |
| 12 json_str = json_file.read() | |
| 13 metadata = json.loads(json_str) | |
| 14 | |
| 15 for marker in metadata["markers"]: | |
| 16 a_set = set(metadata["markers"][marker]["ext"]) | |
| 17 metadata["markers"][marker]["ext"] = a_set | |
| 18 | |
| 19 pkl_output = bz2.BZ2File(args.pkl_output, 'w') | |
| 20 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL) | |
| 21 pkl_output.close() | |
| 22 | |
| 23 | |
| 24 if __name__ == '__main__': | |
| 25 parser = argparse.ArgumentParser() | |
| 26 parser.add_argument('--json_input', required=True) | |
| 27 parser.add_argument('--pkl_output', required=True) | |
| 28 args = parser.parse_args() | |
| 29 | |
| 30 transform_json_to_pkl(args) |