def test_comments(self):
input_str = "([the quick]apple[brown],([fox]banjo,([jumps]cucumber[over the],[really]dogwood)[lazy]eggplant)) rhubarb[dog];"
expected_comments = {
"apple": ["the quick", "brown"],
"banjo": ["fox"],
"cucumber": ["jumps", "over the"],
"dogwood": ["really"],
"eggplant": ["lazy"],
"rhubarb": ["dog"],
}
expected_tokens = [
"(", "apple", ",", "(", "banjo", ",", "(", "cucumber", ",",
"dogwood", ")", "eggplant", ")", ")", "rhubarb", ";"
]
src = StringIO(input_str)
observed_tokens = []
tk = nexusprocessing.NexusTokenizer(src=src)
for token in tk:
if token in expected_comments:
expected_comment = expected_comments[token]
observed_comment = tk.pull_captured_comments()
self.assertEqual(expected_comment, observed_comment)
del expected_comments[token]
observed_tokens.append(token)
self.assertEqual(expected_comments, {})
self.assertEqual(observed_tokens, expected_tokens)
def tree_iter(self,
stream,
taxon_symbol_mapper,
tree_factory):
"""
Iterator that yields trees in NEWICK-formatted source.
Parameters
----------
stream : file or file-like object
A file or file-like object opened for reading.
taxon_namespace : |TaxonNamespace|
Operational taxonomic unit namespace to use for taxon management.
tree_factory : function object
A function that returns a new |Tree| object when called
without arguments.
Returns
-------
iter : :py`collections.Iterator` [|Tree|]
An iterator yielding |Tree| objects constructed based on
data in ``stream``.
"""
nexus_tokenizer = nexusprocessing.NexusTokenizer(stream,
preserve_unquoted_underscores=self.preserve_unquoted_underscores)
while True:
tree = self._parse_tree_statement(
nexus_tokenizer=nexus_tokenizer,
tree_factory=tree_factory,
taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol)
yield tree
if tree is None:
raise StopIteration
def f():
for src_path in src_paths:
if verbose:
sys.stderr.write(" .. {}\n".format(src_path))
src = open(src_path, "rU")
nt = nexusprocessing.NexusTokenizer(src)
for token in nt:
pass
def f():
for src_path in src_paths:
if verbose:
sys.stderr.write(" .. {}\n".format(src_path))
src = open(src_path, "rU")
nt = nexusprocessing.NexusTokenizer(src)
np = newickreader.NewickTreeParser()
while True:
t = np.parse_tree_statement(nt, tree_factory=Tree)
if t is None:
break
def _yield_items_from_stream(self, stream):
nexus_tokenizer = nexusprocessing.NexusTokenizer(
stream,
preserve_unquoted_underscores=self.newick_reader.
preserve_unquoted_underscores)
taxon_symbol_mapper = nexusprocessing.NexusTaxonSymbolMapper(
taxon_namespace=self.attached_taxon_namespace,
enable_lookup_by_taxon_number=False,
case_sensitive=self.newick_reader.case_sensitive_taxon_labels)
while True:
tree = self.newick_reader._parse_tree_statement(
nexus_tokenizer=nexus_tokenizer,
tree_factory=self.tree_factory,
taxon_symbol_map_fn=taxon_symbol_mapper.
require_taxon_for_symbol)
if tree is None:
break
yield tree
def check_tokenization(self, input_str, expected_tokens):
src = StringIO(input_str)
observed = []
for token in nexusprocessing.NexusTokenizer(src=src):
observed.append(token)
self.assertEqual(observed, expected_tokens)