Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/make_json.py @ 0:c3276afba416 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 23 Jul 2015 10:54:53 -0400
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children 065d8a4d74f4
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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1 import json
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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2 import argparse
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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3 import os
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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4 import shutil
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 parser = argparse.ArgumentParser(description='Create data manager json.')
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 parser.add_argument('--db', dest='database', action='store', help='Database name')
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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8 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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10 args = parser.parse_args()
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 def main(args):
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 data_manager_entry = {}
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 data_manager_entry['value'] = args.database.lower()
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 data_manager_entry['name'] = args.database
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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16 data_manager_entry['path'] = '.'
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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17 data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 params = json.loads(open(args.output).read())
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 target_directory = params['output_data'][0]['extra_files_path']
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 os.mkdir(target_directory)
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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21 output_path = os.path.join(os.getcwd(), 'kraken-database')
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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22 for filename in os.listdir(output_path):
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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23 shutil.move(os.path.join(output_path, filename), target_directory)
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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24 file(args.output, 'w').write(json.dumps(data_manager_json))
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 if __name__ == '__main__':
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 main(args)
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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