Mercurial > repos > iuc > data_manager_fetch_refseq

comparison data_manager/fetch_refseq.py @ 4:d58cad5baa70 draft default tip

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"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
comparison
equal deleted inserted replaced
3:f1e545aa76c7 4:d58cad5baa70
139 args = parser.parse_args() 139 args = parser.parse_args()
140 140
141 division_names = args.division_names.split(',') 141 division_names = args.division_names.split(',')
142 mol_types = args.mol_types.split(',') 142 mol_types = args.mol_types.split(',')
143 if args.galaxy_datamanager_filename is not None: 143 if args.galaxy_datamanager_filename is not None:
144 dm_opts = json.loads(open(args.galaxy_datamanager_filename).read()) 144 with open(args.galaxy_datamanager_filename) as fh:
145 dm_opts = json.load(fh)
145 output_directory = dm_opts['output_data'][0]['extra_files_path'] # take the extra_files_path of the first output parameter 146 output_directory = dm_opts['output_data'][0]['extra_files_path'] # take the extra_files_path of the first output parameter
146 data_manager_dict = {} 147 data_manager_dict = {}
147 else: 148 else:
148 output_directory = args.output_directory 149 output_directory = args.output_directory
149 for division_name in division_names: 150 for division_name in division_names:
160 desc = 'RefSeq ' + division_name + ' Release ' + release_num + ' ' + mol_type + ' (' + today_str + ')' 161 desc = 'RefSeq ' + division_name + ' Release ' + release_num + ' ' + mol_type + ' (' + today_str + ')'
161 path = os.path.join(output_directory, fasta_files[i]) 162 path = os.path.join(output_directory, fasta_files[i])
162 _add_data_table_entry(data_manager_dict=data_manager_dict, 163 _add_data_table_entry(data_manager_dict=data_manager_dict,
163 data_table_entry=dict(value=unique_key, dbkey=dbkey, name=desc, path=path), 164 data_table_entry=dict(value=unique_key, dbkey=dbkey, name=desc, path=path),
164 data_table_name='all_fasta') 165 data_table_name='all_fasta')
165 open(args.galaxy_datamanager_filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) 166 with open(args.galaxy_datamanager_filename, 'w') as fh:
167 json.dump(data_manager_dict, fh, sort_keys=True)