Mercurial > repos > bebatut > metaphlan_hclust_heatmap

annotate transform_json_to_pkl.py @ 3:5069e7847ff4 draft default tip

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 b'cf8373aeed58964f1d139a23cd1ec4698683c60e\n'-dirty
author bebatut
date Thu, 02 Mar 2017 11:30:18 -0500
parents 6f69d18bedd9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
1 #!/usr/bin/env python
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
2 # -*- coding: utf-8 -*-
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
3
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
4 import argparse
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
5 import bz2
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
6 import cPickle as pickle
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
7 import json
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
8
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
9
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
10 def transform_json_to_pkl(args):
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
11 with open(args.json_input, 'r') as json_file:
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
12 json_str = json_file.read()
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
13 metadata = json.loads(json_str)
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
14
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
15 for marker in metadata["markers"]:
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
16 a_set = set(metadata["markers"][marker]["ext"])
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
17 metadata["markers"][marker]["ext"] = a_set
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
18
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
19 pkl_output = bz2.BZ2File(args.pkl_output, 'w')
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
20 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
21 pkl_output.close()
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
22
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
23
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
24 if __name__ == '__main__':
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
25 parser = argparse.ArgumentParser()
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
26 parser.add_argument('--json_input', required=True)
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
27 parser.add_argument('--pkl_output', required=True)
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
28 args = parser.parse_args()
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
29
6f69d18bedd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
bebatut
parents:
diff changeset
30 transform_json_to_pkl(args)