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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Tests for NEWICK writing.
"""
import collections
import unittest
import dendropy
import re
from dendropy.test.support import pathmap
from dendropy.test.support import standard_file_test_trees
from dendropy.test.support import compare_and_validate
from dendropy.test.support import dendropytest
def newick_tree_writer_test_tree(
has_leaf_node_taxa=True,
has_leaf_node_labels=True,
has_internal_node_taxa=True,
has_internal_node_labels=True,
has_edge_lengths=True,
label_pool=None,
label_separator=' ',
):
anodes = set()
tree = dendropy.Tree()
tns = tree.taxon_namespace
a = tree.seed_node.new_child()
b = tree.seed_node.new_child()
a1 = a.new_child()
a2 = a.new_child()
b1 = b.new_child()
b2 = b.new_child()
anodes.add(tree.seed_node)
anodes.add(a)
anodes.add(b)
anodes.add(a1)
anodes.add(a2)
anodes.add(b1)
anodes.add(b2)
if label_pool is None:
label_pool = [chr(i) for i in range(ord('a'), ord('z')+1)]
labeller = iter(label_pool)
for nd_idx, nd in enumerate(anodes):
expected_label_parts = collections.defaultdict(list)
is_leaf = nd.is_leaf()
if ( (is_leaf and has_leaf_node_taxa)
or ((not is_leaf) and has_internal_node_taxa) ):
label = next(labeller)
tx = tree.taxon_namespace.require_taxon(label=label)
nd.taxon = tx
expected_label_parts[ (False, True ) ].append(label)
expected_label_parts[ (False, False) ].append(label)
if ( (is_leaf and has_leaf_node_labels)
or ((not is_leaf) and has_internal_node_labels) ):
label = next(labeller)
nd.label = label
expected_label_parts[ (True, False) ].append(label)
expected_label_parts[ (False, False) ].append(label)
nd.expected_label = collections.defaultdict(lambda: None)
for k in expected_label_parts:
nd.expected_label[k] = label_separator.join(expected_label_parts[k])
if has_edge_lengths:
nd.edge.length = nd_idx
return tree
class NewickTreeWriterDefaultTest(
standard_file_test_trees.NewickTestTreesChecker,
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls,
is_metadata_extracted=True,
)
def test_roundtrip_full(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-annotated-x10a'
tree_filepath = standard_file_test_trees._TREE_FILEPATHS["newick"][tree_file_title]
tree1 = dendropy.Tree.get_from_path(
tree_filepath,
"newick",
extract_comment_metadata=True,
store_tree_weights=True,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False,
)
kwargs = {
"suppress_leaf_taxon_labels" : False , # default: False ,
"suppress_leaf_node_labels" : True , # default: True ,
"suppress_internal_taxon_labels" : False , # default: False ,
"suppress_internal_node_labels" : True , # default: False ,
"suppress_rooting" : False , # default: False ,
"suppress_edge_lengths" : False , # default: False ,
"unquoted_underscores" : False , # default: False ,
"preserve_spaces" : False , # default: False ,
"store_tree_weights" : False , # default: False ,
"suppress_annotations" : False , # default: True ,
"annotations_as_nhx" : False , # default: False ,
"suppress_item_comments" : False , # default: True ,
"node_label_element_separator" : ' ' , # default: ' ' ,
"node_label_compose_fn" : None , # default: None ,
"edge_label_compose_fn" : None , # default: None ,
}
s = self.write_out_validate_equal_and_return(
tree1, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
extract_comment_metadata=True,
store_tree_weights=True,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
)
self.compare_to_reference_by_title_and_index(
tree=tree2,
tree_file_title=tree_file_title,
reference_tree_idx=0)
# suppress_internal_node_taxa=False,
# suppress_leaf_node_taxa=False,
# is_metadata_extracted=True,
# is_coerce_metadata_values_to_string=True,
# is_distinct_nodes_and_edges_representation=False)
class NewickTreeWriterGeneralOptionsTests(
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
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, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
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_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, "newick", kwargs)
if suppress_rooting:
self.assertFalse(s.startswith("[&R]") or s.startswith("[&U]"))
else:
if rooted_state is True:
self.assertTrue(s.startswith("[&R]"))
elif rooted_state is False:
self.assertTrue(s.startswith("[&U]"))
else:
self.assertFalse(s.startswith("[&R]") or s.startswith("[&U]"))
tree2 = dendropy.Tree.get_from_string(
s, "newick", 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)
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, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s, "newick", 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_unquoted_underscores(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 unquoted_underscores in (True, False):
kwargs = {
"unquoted_underscores": unquoted_underscores,
}
s = self.write_out_validate_equal_and_return(
tree1, "newick", kwargs)
for preserve_underscores in (True, False):
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
suppress_internal_node_taxa=False,
preserve_underscores=preserve_underscores)
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 unquoted_underscores:
if preserve_underscores:
expected_label = original_label
else:
expected_label = original_label.replace("_", " ")
else:
expected_label = original_label
self.assertEqual(nd2.taxon.label, expected_label)
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, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
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_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, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
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_suppress_annotations(self):
tree1 = dendropy.Tree()
a1 = tree1.seed_node.new_child()
a2 = tree1.seed_node.new_child()
tree1.annotations.add_new("t", 1)
for nd in tree1:
nd.annotations.add_new("a", 1)
nd.edge.annotations.add_new("b", 2)
for suppress_annotations in (True, False):
for annotations_as_nhx in (True, False):
kwargs = {
"suppress_annotations" : suppress_annotations,
"annotations_as_nhx" : annotations_as_nhx,
}
s = self.write_out_validate_equal_and_return(
tree1, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
extract_comment_metadata=True)
if suppress_annotations:
self.assertFalse(tree2.has_annotations)
for nd in tree2:
self.assertFalse(nd.has_annotations)
else:
if annotations_as_nhx:
self.assertEqual(s.count("[&&NHX"), 7)
# self.assertEqual(len(re.findall(r"\[&&NHX", s)), 7)
else:
self.assertEqual(s.count("[&&NHX"), 0)
self.assertEqual(s.count("[&"), 7)
# self.assertEqual(len(re.findall(r"\[&&NHX", s)), 0)
# self.assertEqual(len(re.findall(r"\[&.*?\]", s)), 7)
self.assertTrue(tree2.has_annotations)
self.assertEqual(tree2.annotations.get_value("t"), '1')
for nd in tree2:
self.assertTrue(nd.has_annotations)
self.assertEqual(nd.annotations.get_value("a"), '1')
self.assertEqual(nd.annotations.get_value("b"), '2')
def test_suppress_item_comments(self):
tree1 = dendropy.Tree()
a1 = tree1.seed_node.new_child()
a2 = tree1.seed_node.new_child()
tree1.comments.append("t1")
for nd in tree1:
nd.comments.append("n1")
nd.edge.comments.append("e1")
for suppress_item_comments in (True, False):
kwargs = {
"suppress_item_comments" : suppress_item_comments,
}
s = self.write_out_validate_equal_and_return(
tree1, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
extract_comment_metadata=False)
if suppress_item_comments:
self.assertEqual(tree2.comments, [])
for nd in tree2:
self.assertEqual(nd.comments, [])
self.assertEqual(nd.edge.comments, [])
else:
self.assertEqual(tree2.comments, ["t1"])
for nd in tree2:
self.assertEqual(nd.comments, ["n1", "e1"])
def test_node_label_compose_fn(self):
tree1 = dendropy.Tree()
a1 = tree1.seed_node.new_child(label="a1")
a1.taxon = tree1.taxon_namespace.require_taxon("hula")
a2 = tree1.seed_node.new_child(label="a1")
a2.taxon = tree1.taxon_namespace.require_taxon("hoop")
f = lambda x: "zzz"
kwargs = {
"suppress_leaf_taxon_labels" : False ,
"suppress_leaf_node_labels" : False ,
"suppress_internal_taxon_labels" : False ,
"suppress_internal_node_labels" : False ,
"node_label_compose_fn" : f,
}
s = self.write_out_validate_equal_and_return(
tree1, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
suppress_leaf_node_taxa=True,
suppress_internal_node_taxa=True)
for nd in tree2:
self.assertEqual(nd.label, "zzz")
def test_edge_label_compose_fn(self):
tree1 = dendropy.Tree()
tree1.seed_node.edge.length = 1
a1 = tree1.seed_node.new_child(label="a1", edge_length=1)
a2 = tree1.seed_node.new_child(label="a1", edge_length=1)
f = lambda x: 1000
kwargs = {
"edge_label_compose_fn" : f,
}
s = self.write_out_validate_equal_and_return(
tree1, "newick", kwargs)
tree2 = dendropy.Tree.get_from_string(
s,
"newick",
suppress_leaf_node_taxa=True,
suppress_internal_node_taxa=True)
for nd in tree2:
self.assertEqual(nd.edge.length, 1000)
if __name__ == "__main__":
unittest.main()
|
