diff --git a/src/sourmash/search.py b/src/sourmash/search.py index 045d567f22..31f75c28b3 100644 --- a/src/sourmash/search.py +++ b/src/sourmash/search.py @@ -29,8 +29,8 @@ def search_databases(query, databases, threshold, do_containment, best_only, ignore_abundance, unload_data=False): results = [] found_md5 = set() - for (obj, _) in databases: - search_iter = obj.search(query, threshold=threshold, + for db in databases: + search_iter = db.search(query, threshold=threshold, do_containment=do_containment, ignore_abundance=ignore_abundance, best_only=best_only, @@ -85,8 +85,8 @@ def _find_best(dblist, query, threshold_bp): threshold_bp = int(threshold_bp / query_scaled) * query_scaled # search across all databases - for (obj, _) in dblist: - for cont, match, fname in obj.gather(query, threshold_bp=threshold_bp): + for db in dblist: + for cont, match, fname in db.gather(query, threshold_bp=threshold_bp): assert cont # all matches should be nonzero. # note, break ties based on name, to ensure consistent order. diff --git a/src/sourmash/sourmash_args.py b/src/sourmash/sourmash_args.py index 3f57898cec..aaf1536c7d 100644 --- a/src/sourmash/sourmash_args.py +++ b/src/sourmash/sourmash_args.py @@ -283,7 +283,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None) siglist = _select_sigs(db, moltype=query_moltype, ksize=query_ksize) siglist = filter_compatible_signatures(query, siglist, 1) linear = LinearIndex(siglist, filename=filename) - databases.append((linear, filename)) + databases.append(linear) n_signatures += len(linear) @@ -293,7 +293,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None) is_similarity_query): sys.exit(-1) - databases.append((db, filename)) + databases.append(db) notify('loaded SBT {}', filename, end='\r') n_databases += 1 @@ -306,7 +306,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None) notify('loaded LCA {}', filename, end='\r') n_databases += 1 - databases.append((db, filename)) + databases.append(db) # signature file elif dbtype == DatabaseType.SIGLIST: @@ -318,7 +318,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None) sys.exit(-1) linear = LinearIndex(siglist, filename=filename) - databases.append((linear, filename)) + databases.append(linear) notify('loaded {} signatures from {}', len(linear), filename, end='\r')