Mercurial > repos > iuc > data_manager_mash_sketch_builder

comparison data_manager/mash_sketch_builder.py @ 2:ce1d5c8d5bff draft

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/data_managers/data_manager_mash_sketch_builder/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:50:56 +0000
parents b6016642539d
children
comparison
equal deleted inserted replaced
1:b6016642539d 2:ce1d5c8d5bff
57 parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch') 57 parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch')
58 parser.add_argument('--threads', dest='threads', default=1, help='threads') 58 parser.add_argument('--threads', dest='threads', default=1, help='threads')
59 parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch') 59 parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch')
60 args = parser.parse_args() 60 args = parser.parse_args()
61 61
62 data_manager_input = json.loads(open(args.data_manager_json).read()) 62 with open(args.data_manager_json) as fh:
63 data_manager_input = json.load(fh)
63 64
64 target_directory = data_manager_input['output_data'][0]['extra_files_path'] 65 target_directory = data_manager_input['output_data'][0]['extra_files_path']
65 66
66 try: 67 try:
67 os.mkdir(target_directory) 68 os.mkdir(target_directory)
86 mash_sketch_args, 87 mash_sketch_args,
87 args.sketch_name, 88 args.sketch_name,
88 target_directory, 89 target_directory,
89 ) 90 )
90 91
91 open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True)) 92 with open(args.data_manager_json, 'w') as fh:
93 json.dump(data_manager_output, fh, sort_keys=True)
92 94
93 95
94 if __name__ == "__main__": 96 if __name__ == "__main__":
95 main() 97 main()