Mercurial > repos > iuc > humann2_rna_dna_norm

annotate transform_json_to_pkl.py @ 5:de70d23958de draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 07:01:39 +0000
parents c8ef30c8451d
children
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
1 #!/usr/bin/env python
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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2 # -*- coding: utf-8 -*-
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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4 import argparse
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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5 import bz2
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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6 import cPickle as pickle
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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7 import json
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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9
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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10 def transform_json_to_pkl(args):
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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11 with open(args.json_input, 'r') as json_file:
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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12 json_str = json_file.read()
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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13 metadata = json.loads(json_str)
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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15 for marker in metadata["markers"]:
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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16 a_set = set(metadata["markers"][marker]["ext"])
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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17 metadata["markers"][marker]["ext"] = a_set
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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19 pkl_output = bz2.BZ2File(args.pkl_output, 'w')
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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20 pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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21 pkl_output.close()
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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24 if __name__ == '__main__':
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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25 parser = argparse.ArgumentParser()
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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26 parser.add_argument('--json_input', required=True)
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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27 parser.add_argument('--pkl_output', required=True)
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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28 args = parser.parse_args()
c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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30 transform_json_to_pkl(args)