Mercurial > repos > iuc > humann2_barplot

annotate transform_json_to_pkl.py @ 2:fc30f1dec9b9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908"
author iuc
date Sat, 25 Jan 2020 18:24:25 -0500
parents efd98a5e8255
children
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efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
1 #!/usr/bin/env python
efd98a5e8255 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 -*-
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
4 import argparse
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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5 import bz2
efd98a5e8255 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
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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7 import json
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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9
efd98a5e8255 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):
efd98a5e8255 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:
efd98a5e8255 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()
efd98a5e8255 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)
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 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"]:
efd98a5e8255 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"])
efd98a5e8255 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
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 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')
efd98a5e8255 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)
efd98a5e8255 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()
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 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__':
efd98a5e8255 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()
efd98a5e8255 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)
efd98a5e8255 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)
efd98a5e8255 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()
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
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efd98a5e8255 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)