Mercurial > repos > iuc > data_manager_build_bracken_database

comparison data_manager/bracken_build_database.py @ 2:fd5830f88314 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:45:23 +0000
parents c2e4127fb5bf
children 3c7d2c84cb09
comparison
equal deleted inserted replaced
1:9059edc96a85 2:fd5830f88314
53 parser.add_argument('--read-len', dest='read_len', help='Read length') 53 parser.add_argument('--read-len', dest='read_len', help='Read length')
54 parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database') 54 parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database')
55 parser.add_argument('--database-name', dest='database_name', help='Database Name') 55 parser.add_argument('--database-name', dest='database_name', help='Database Name')
56 args = parser.parse_args() 56 args = parser.parse_args()
57 57
58 data_manager_input = json.loads(open(args.data_manager_json).read()) 58 with open(args.data_manager_json) as fh:
59 data_manager_input = json.load(fh)
59 60
60 target_directory = data_manager_input['output_data'][0]['extra_files_path'] 61 target_directory = data_manager_input['output_data'][0]['extra_files_path']
61 62
62 bracken_build_args = { 63 bracken_build_args = {
63 'threads': args.threads, 64 'threads': args.threads,
67 } 68 }
68 69
69 try: 70 try:
70 os.mkdir(target_directory) 71 os.mkdir(target_directory)
71 except OSError as exc: 72 except OSError as exc:
72 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): 73 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
73 pass 74 pass
74 else: 75 else:
75 raise 76 raise
76 77
77 data_manager_output = {} 78 data_manager_output = {}
80 target_directory, 81 target_directory,
81 bracken_build_args, 82 bracken_build_args,
82 args.database_name, 83 args.database_name,
83 ) 84 )
84 85
85 with open(args.data_manager_json, 'w') as out: 86 with open(args.data_manager_json, 'w') as fh:
86 out.write(json.dumps(data_manager_output, sort_keys=True)) 87 json.dump(data_manager_output, fh, sort_keys=True)
87 88
88 89
89 if __name__ == "__main__": 90 if __name__ == "__main__":
90 main() 91 main()