Mercurial > repos > bebatut > metaphlan2
comparison transform_json_to_pkl.py @ 0:d2448d2bf1f8 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
| author | bebatut |
|---|---|
| date | Wed, 01 Jun 2016 10:45:26 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:d2448d2bf1f8 |
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| 1 #!/usr/bin/env python | |
| 2 # -*- coding: utf-8 -*- | |
| 3 | |
| 4 import cPickle as pickle | |
| 5 import bz2 | |
| 6 import json | |
| 7 import argparse | |
| 8 | |
| 9 def transform_json_to_pkl(args): | |
| 10 with open(args.json_input, 'r') as json_file: | |
| 11 json_str = json_file.read() | |
| 12 metadata = json.loads(json_str) | |
| 13 | |
| 14 for marker in metadata["markers"]: | |
| 15 metadata["markers"][marker]["ext"] = set(metadata["markers"][marker]["ext"]) | |
| 16 | |
| 17 pkl_output = bz2.BZ2File(args.pkl_output, 'w') | |
| 18 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL) | |
| 19 pkl_output.close() | |
| 20 | |
| 21 if __name__ == '__main__': | |
| 22 parser = argparse.ArgumentParser() | |
| 23 parser.add_argument('--json_input', required=True) | |
| 24 parser.add_argument('--pkl_output', required=True) | |
| 25 | |
| 26 args = parser.parse_args() | |
| 27 | |
| 28 transform_json_to_pkl(args) |