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
