Mercurial > repos > iuc > data_manager_fetch_refseq
diff data_manager/fetch_refseq.py @ 4:d58cad5baa70 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:49:04 +0000 |
| parents | 8b91891ae805 |
| children |
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--- a/data_manager/fetch_refseq.py Sun Apr 19 14:44:09 2020 -0400 +++ b/data_manager/fetch_refseq.py Sun Nov 22 12:49:04 2020 +0000 @@ -141,7 +141,8 @@ division_names = args.division_names.split(',') mol_types = args.mol_types.split(',') if args.galaxy_datamanager_filename is not None: - dm_opts = json.loads(open(args.galaxy_datamanager_filename).read()) + with open(args.galaxy_datamanager_filename) as fh: + dm_opts = json.load(fh) output_directory = dm_opts['output_data'][0]['extra_files_path'] # take the extra_files_path of the first output parameter data_manager_dict = {} else: @@ -162,4 +163,5 @@ _add_data_table_entry(data_manager_dict=data_manager_dict, data_table_entry=dict(value=unique_key, dbkey=dbkey, name=desc, path=path), data_table_name='all_fasta') - open(args.galaxy_datamanager_filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) + with open(args.galaxy_datamanager_filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True)