diff --git a/upimapi.py b/upimapi.py index 2a571fe..f63ecd6 100644 --- a/upimapi.py +++ b/upimapi.py @@ -48,7 +48,7 @@ def get_arguments(self): "'output' parameter just for that specific file") parser.add_argument("-cols", "--columns", default='', help="List of UniProt columns to obtain information from (separated by &)") - parser.add_argument("-dbs", "--annotation-databases", default='', + parser.add_argument("-dbs", "--databases", default='', help="List of databases to cross-check with UniProt information (separated by &)") parser.add_argument("--blast", action="store_true", default=False, help="If input file is in BLAST TSV format (will consider one ID per line if not set)") @@ -218,8 +218,7 @@ def uniprot_fasta_workflow(self, all_ids, output, max_iter=5, step=1000, sleep_t ids_missing = list(set(all_ids) - set(ids_done)) tries = 0 - ids_done = ([ide.split('|')[1] for ide in self.get_fasta_ids(output)] - if os.path.isfile(output) else list()) + ids_done = ([ide.split('|')[1] for ide in self.get_fasta_ids(output)] if os.path.isfile(output) else list()) while len(ids_done) < len(all_ids) and tries < max_iter: print('Checking which IDs are missing information.') ids_missing = list(set([ide for ide in tqdm(all_ids, desc='Checking which IDs are missing information.') @@ -381,7 +380,7 @@ def upimapi(self): columns = args.columns.split('&') if args.columns != '' else list() databases = args.databases.split('&') if args.databases != '' else list() - if hasattr(args, "output_table"): + if args.output_table: table_output = args.output_table pathlib.Path('/'.join(args.output_table.split('/')[:-1])).mkdir(parents=True, exist_ok=True) else: