def test_store_tree_weights(self):
tree1 = newick_tree_writer_test_tree(
has_leaf_node_labels=False,
has_internal_node_labels=False)
for store_tree_weights in (True, False):
for weight in (None, "23.0", "1/2", 1.0):
tree1.weight = weight
kwargs = {
"store_tree_weights": store_tree_weights,
}
s = self.write_out_validate_equal_and_return(
tree1, "nexus", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"nexus",
store_tree_weights=True)
if store_tree_weights and weight is not None:
self.assertTrue("[&W " in s)
try:
w = float(weight)
except ValueError:
w = eval("/".join(str(float(w)) for w in weight.split("/")))
self.assertEqual(tree2.weight, w)
else:
self.assertFalse("[&W " in s)
self.assertEqual(tree2.weight, 1.0) # default weight
def test_preserve_spaces(self):
tree1 = newick_tree_writer_test_tree(
has_leaf_node_labels=False,
has_internal_node_labels=False)
for taxon in tree1.taxon_namespace:
taxon.label = "{label} {label}".format(label=taxon.label)
for preserve_spaces in (True, False):
kwargs = {
"preserve_spaces": preserve_spaces,
}
s = self.write_out_validate_equal_and_return(
tree1, "nexus", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"nexus",
suppress_internal_node_taxa=False,
preserve_underscores=True)
nodes1 = [nd for nd in tree1]
nodes2 = [nd for nd in tree2]
self.assertEqual(len(nodes1), len(nodes2))
for nd1, nd2 in zip(nodes1, nodes2):
original_label = nd1.taxon.label
if preserve_spaces:
expected_label = original_label
else:
expected_label = original_label.replace(" ", "_")
self.assertEqual(nd2.taxon.label, expected_label)
def test_node_labeling(self):
for has_leaf_node_taxa in (True, False):
for has_leaf_node_labels in (True, False):
for has_internal_node_taxa in (True, False):
for has_internal_node_labels in (True, False):
for label_separator in (' ', '$$$'):
tree = newick_tree_writer_test_tree(
has_leaf_node_taxa=has_leaf_node_taxa,
has_leaf_node_labels=has_leaf_node_labels,
has_internal_node_taxa=has_internal_node_taxa,
has_internal_node_labels=has_internal_node_labels,
label_separator=label_separator,
)
for suppress_leaf_taxon_labels in (True, False):
for suppress_leaf_node_labels in (True, False):
for suppress_internal_taxon_labels in (True, False):
for suppress_internal_node_labels in (True, False):
kwargs = {
"suppress_leaf_taxon_labels" : suppress_leaf_taxon_labels,
"suppress_leaf_node_labels" : suppress_leaf_node_labels,
"suppress_internal_taxon_labels" : suppress_internal_taxon_labels,
"suppress_internal_node_labels" : suppress_internal_node_labels,
"node_label_element_separator" : label_separator,
}
s = self.write_out_validate_equal_and_return(
tree, "nexus", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"nexus",
extract_comment_metadata=True,
store_tree_weights=True,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True,
)
nodes1 = [nd for nd in tree]
nodes2 = [nd for nd in tree2]
self.assertEqual(len(nodes1), len(nodes2))
for nd1, nd2 in zip(nodes1, nodes2):
is_leaf = nd1.is_leaf()
self.assertEqual(nd2.is_leaf(), is_leaf)
if is_leaf:
self.assertEqual(nd2.label,
nd1.expected_label[(suppress_leaf_taxon_labels, suppress_leaf_node_labels)])
else:
self.assertEqual(nd2.label,
nd1.expected_label[ (suppress_internal_taxon_labels, suppress_internal_node_labels) ])
def test_edge_lengths(self):
tree1 = newick_tree_writer_test_tree()
for suppress_edge_lengths in (True, False):
kwargs = {
"suppress_edge_lengths": suppress_edge_lengths,
}
s = self.write_out_validate_equal_and_return(
tree1, "nexus", kwargs)
tree2 = dendropy.Tree.get_from_string(
s, "nexus", rooting=None)
nodes1 = [nd for nd in tree1]
nodes2 = [nd for nd in tree2]
self.assertEqual(len(nodes1), len(nodes2))
for nd1, nd2 in zip(nodes1, nodes2):
if suppress_edge_lengths:
self.assertIs(nd2.edge.length, None)
else:
self.assertEqual(nd2.edge.length, nd1.edge.length)
def test_rooting_token(self):
tree1 = newick_tree_writer_test_tree()
for rooted_state in (None, True, False):
tree1.is_rooted = rooted_state
for suppress_rooting in (True, False):
kwargs = {
"suppress_rooting": suppress_rooting,
}
s = self.write_out_validate_equal_and_return(
tree1, "nexus", kwargs)
tree2 = dendropy.Tree.get_from_string(
s, "nexus", rooting=None)
if suppress_rooting:
self.assertTrue(tree2.is_rootedness_undefined)
else:
if rooted_state is True:
self.assertTrue(tree2.is_rooted)
self.assertFalse(tree2.is_unrooted)
elif rooted_state is False:
self.assertFalse(tree2.is_rooted)
self.assertTrue(tree2.is_unrooted)
else:
self.assertTrue(tree2.is_rootedness_undefined)
