def test_taxonomy_subset_zaire(request, tmpdir_factory): data_dir = join(util.file.get_test_input_path(), 'TestMetagenomicsSimple') db_dir = join(data_dir, 'db', 'taxonomy') sub_dir = str(tmpdir_factory.mktemp('taxonomy_subset')) # Zaire species metagenomics.subset_taxonomy(db_dir, sub_dir, whitelistTaxids=[], whitelistTreeTaxids=[186538]) tax_db = metagenomics.TaxonomyDb(sub_dir, load_nodes=True, load_names=True) assert 186538 in tax_db.parents # Zaire species assert 186540 not in tax_db.parents # Sudan species assert 2 not in tax_db.parents # Bacteria
def taxa_db(parents, names, ranks): db = metagenomics.TaxonomyDb() db.parents = parents db.names = names db.ranks = ranks return db
def taxa_db_simple(): db = metagenomics.TaxonomyDb() db.gis = {1: 2, 2: 3, 3: 4, 4: 5} db.parents = {1: 1, 2: 1, 3: 2, 4: 3, 5: 4} return db