Mercurial > repos > iuc > humann2_rename_table

annotate transform_json_to_pkl.py @ 4:939d053a96b3 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/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
author iuc
date Mon, 01 Feb 2021 18:19:04 +0000
parents dd4b5b9daf6b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
1 #!/usr/bin/env python
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
2 # -*- coding: utf-8 -*-
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
3
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
4 import argparse
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
5 import bz2
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
6 import cPickle as pickle
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
7 import json
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
8
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
9
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
10 def transform_json_to_pkl(args):
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
11 with open(args.json_input, 'r') as json_file:
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
12 json_str = json_file.read()
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
13 metadata = json.loads(json_str)
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
14
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
15 for marker in metadata["markers"]:
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
16 a_set = set(metadata["markers"][marker]["ext"])
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
17 metadata["markers"][marker]["ext"] = a_set
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
18
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
19 pkl_output = bz2.BZ2File(args.pkl_output, 'w')
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
20 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
21 pkl_output.close()
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
22
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
23
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
24 if __name__ == '__main__':
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
25 parser = argparse.ArgumentParser()
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
26 parser.add_argument('--json_input', required=True)
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
27 parser.add_argument('--pkl_output', required=True)
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
28 args = parser.parse_args()
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
29
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff changeset
30 transform_json_to_pkl(args)