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)
