Mercurial > repos > iuc > metaphlan2

annotate transform_json_to_pkl.py @ 0:a12c7f019bdf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
author iuc
date Sat, 04 Mar 2017 12:22:28 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
1 #!/usr/bin/env python
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
2 # -*- coding: utf-8 -*-
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
3
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
4 import argparse
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
5 import bz2
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
6 import cPickle as pickle
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
7 import json
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
8
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
9
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
10 def transform_json_to_pkl(args):
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
11 with open(args.json_input, 'r') as json_file:
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
12 json_str = json_file.read()
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
13 metadata = json.loads(json_str)
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
14
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
15 for marker in metadata["markers"]:
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
16 a_set = set(metadata["markers"][marker]["ext"])
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
17 metadata["markers"][marker]["ext"] = a_set
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
18
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
19 pkl_output = bz2.BZ2File(args.pkl_output, 'w')
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
20 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
21 pkl_output.close()
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
22
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
23
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
24 if __name__ == '__main__':
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
25 parser = argparse.ArgumentParser()
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
26 parser.add_argument('--json_input', required=True)
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
27 parser.add_argument('--pkl_output', required=True)
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
28 args = parser.parse_args()
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
29
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
30 transform_json_to_pkl(args)