def __init__(self, files=None, taxon_namespace=None, tree_type=None, **kwargs): """ Parameters ---------- files : iterable of sources Iterable of sources, which can either be strings specifying file paths or file-like objects open for reading. If a source element is a stringm then it is assumed to be a path to a file. Otherwise, the source is assumed to be a file-like object. taxon_namespace : |TaxonNamespace| instance The operational taxonomic unit concept namespace to use to manage taxon definitions. \*\*kwargs : keyword arguments These will be passed directly to the base `newickreader.NexusReader` class. See `newickreader.NexusReader` for details. """ ioservice.TreeDataYielder.__init__(self, files=files, taxon_namespace=taxon_namespace, tree_type=tree_type) self.newick_reader = newickreader.NewickReader(**kwargs)
def test_legacy_keywords(self): for kwset in self.legacy_kw: with warnings.catch_warnings(record=True) as w: # Cause all warnings to always be triggered. warnings.simplefilter("always") # Trigger a warning. kwargs = {kwset[0]: kwset[1]} nr = newickreader.NewickReader(**kwargs) self.assertEqual(nr.rooting, kwset[2])
def test_with_rooted_token_ucase(self): nr = newickreader.NewickReader(rooting="force-rooted") self.assertIs(nr._parse_tree_rooting_state("&R"), True)
def test_with_meaningless_token_ucase(self): nr = newickreader.NewickReader(rooting="force-unrooted") self.assertIs(nr._parse_tree_rooting_state("zz"), False)
def test_with_rooted_token_lcase(self): nr = newickreader.NewickReader(rooting="force-unrooted") self.assertIs(nr._parse_tree_rooting_state("&r"), False)
def test_multiple_keyword_error(self): with self.assertRaises(ValueError): nr = newickreader.NewickReader(as_rooted=True, as_unrooted=True)
def test_with_meaningless_token_ucase(self): nr = newickreader.NewickReader(rooting="default-rooted") self.assertIs(nr._parse_tree_rooting_state("zz"), True)
def test_with_unrooted_token_ucase(self): nr = newickreader.NewickReader(rooting="default-rooted") self.assertIs(nr._parse_tree_rooting_state("&U"), False)
def test_with_no_token2(self): nr = newickreader.NewickReader(rooting="default-rooted") self.assertIs(nr._parse_tree_rooting_state(), True)
def test_with_no_token(self): nr = newickreader.NewickReader(rooting="default-unrooted") self.assertIs(nr._parse_tree_rooting_state(""), False)