Mercurial > repos > bebatut > metaphlan2

comparison transform_json_to_pkl.py @ 31:83f06bee818c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
author bebatut
date Tue, 21 Feb 2017 12:29:37 -0500
parents 713a83023626
children
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30:99fe591b59fb 31:83f06bee818c
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*- 2 # -*- coding: utf-8 -*-
3 3
4 import argparse
5 import bz2
4 import cPickle as pickle 6 import cPickle as pickle
5 import bz2
6 import json 7 import json
7 import argparse 8
8 9
9 def transform_json_to_pkl(args): 10 def transform_json_to_pkl(args):
10 with open(args.json_input, 'r') as json_file: 11 with open(args.json_input, 'r') as json_file:
11 json_str = json_file.read() 12 json_str = json_file.read()
12 metadata = json.loads(json_str) 13 metadata = json.loads(json_str)
13 14
14 for marker in metadata["markers"]: 15 for marker in metadata["markers"]:
15 metadata["markers"][marker]["ext"] = set(metadata["markers"][marker]["ext"]) 16 a_set = set(metadata["markers"][marker]["ext"])
17 metadata["markers"][marker]["ext"] = a_set
16 18
17 pkl_output = bz2.BZ2File(args.pkl_output, 'w') 19 pkl_output = bz2.BZ2File(args.pkl_output, 'w')
18 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL) 20 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
19 pkl_output.close() 21 pkl_output.close()
20 22
23
21 if __name__ == '__main__': 24 if __name__ == '__main__':
22 parser = argparse.ArgumentParser() 25 parser = argparse.ArgumentParser()
23 parser.add_argument('--json_input', required=True) 26 parser.add_argument('--json_input', required=True)
24 parser.add_argument('--pkl_output', required=True) 27 parser.add_argument('--pkl_output', required=True)
25
26 args = parser.parse_args() 28 args = parser.parse_args()
27 29
28 transform_json_to_pkl(args) 30 transform_json_to_pkl(args)