def testTreeListReaderSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
newick_str = datagen.reference_tree_list_newick_string()
t_tree_list = dendropy.TreeList.get_from_string(newick_str, 'newick', taxon_set=ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testTreeListReaderSameTaxa(self):
ref_tree_list = datagen.reference_tree_list()
newick_str = datagen.reference_tree_list_newick_string()
t_tree_list = dendropy.TreeList.get_from_string(
newick_str, 'newick', taxon_set=ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testTreeListReaderDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
newick_str = datagen.reference_tree_list_newick_string()
t_tree_list = dendropy.TreeList.get_from_string(newick_str, 'newick')
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None,
ignore_taxon_order=True)
def testTreeListReaderDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
newick_str = datagen.reference_tree_list_newick_string()
t_tree_list = dendropy.TreeList.get_from_string(newick_str, 'newick')
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None,
ignore_taxon_order=True)
def testReferenceTreeList(self):
tlist1 = datagen.reference_tree_list()
ref_trees_newick = [n.strip() for n in datagen.reference_tree_list_newick_string().split(";")]
ref_node_labels = datagen.reference_tree_list_postorder_node_labels()
ref_node_rels = datagen.reference_tree_list_node_relationships()
for ti, t1 in enumerate(tlist1):
t1.assign_node_labels_from_taxon_or_oid()
t1_newick = t1.as_newick_string(include_internal_labels=True, preserve_spaces=True)
self.assertEqual(t1_newick, ref_trees_newick[ti])
node_labels1 = [nd.label for nd in t1.postorder_node_iter()]
self.assertEqual(node_labels1, ref_node_labels[ti])
nodes1 = [nd for nd in t1.postorder_node_iter()]
for ndi, nd1 in enumerate(nodes1):
ndrel = ref_node_rels[ti][nd1.label]
ndrel.test_node(self, nd1)
def testReferenceTreeList(self):
tlist1 = datagen.reference_tree_list()
ref_trees_newick = [
n.strip()
for n in datagen.reference_tree_list_newick_string().split(";")
]
ref_node_labels = datagen.reference_tree_list_postorder_node_labels()
ref_node_rels = datagen.reference_tree_list_node_relationships()
for ti, t1 in enumerate(tlist1):
t1.assign_node_labels_from_taxon_or_oid()
t1_newick = t1.as_newick_string(include_internal_labels=True,
preserve_spaces=True)
self.assertEqual(t1_newick, ref_trees_newick[ti])
node_labels1 = [nd.label for nd in t1.postorder_node_iter()]
self.assertEqual(node_labels1, ref_node_labels[ti])
nodes1 = [nd for nd in t1.postorder_node_iter()]
for ndi, nd1 in enumerate(nodes1):
ndrel = ref_node_rels[ti][nd1.label]
ndrel.test_node(self, nd1)
