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)