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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.
##
##############################################################################
import sys
import json
import random
import dendropy
import copy
from dendropy.test.support import pathmap
if sys.hexversion < 0x03040000:
from dendropy.utility.filesys import pre_py34_open as open
from dendropy.utility.messaging import get_logger
_LOG = get_logger(__name__)
tree_file_titles = [
"dendropy-test-trees-multifurcating-rooted-annotated",
"dendropy-test-trees-multifurcating-rooted",
"dendropy-test-trees-multifurcating-unrooted",
"dendropy-test-trees-n10-rooted-treeshapes",
"dendropy-test-trees-n12-x2",
"dendropy-test-trees-n14-unrooted-treeshapes",
"dendropy-test-trees-n33-unrooted-annotated-x10a",
"dendropy-test-trees-n33-unrooted-x10a",
"dendropy-test-trees-n33-unrooted-x10b",
"dendropy-test-trees-n33-unrooted-x100a",
]
schema_extension_map = {
"nexml" : "nexml",
"newick" : "newick",
"nexus" : "nexus",
"json" : "json",
"nexus-metadata-comments" : "nexus-metadata-comments.json",
}
_TREE_FILEPATHS = {}
_TREE_REFERENCES = {}
_NEXUS_METADATA_COMMENTS = {}
def setup_module():
for schema in schema_extension_map:
_TREE_FILEPATHS[schema] = {}
for tree_file_title in tree_file_titles:
tf = "{}.{}".format(tree_file_title, schema_extension_map[schema])
_TREE_FILEPATHS[schema][tree_file_title] = pathmap.tree_source_path(tf)
for tree_file_title in tree_file_titles:
with open(_TREE_FILEPATHS["json"][tree_file_title]) as src:
_TREE_REFERENCES[tree_file_title] = json.load(src)
if "annotated" in tree_file_title:
with open(_TREE_FILEPATHS["nexus-metadata-comments"][tree_file_title]) as src:
_NEXUS_METADATA_COMMENTS[tree_file_title] = json.load(src)
setup_module()
class StandardTestTreesChecker(object):
def preprocess_tree_to_be_checked(self, tree):
pass
def compare_annotations_to_json_metadata_dict(self,
item,
expected_metadata):
item_annotations_as_dict = item.annotations.values_as_dict()
if self.__class__.is_coerce_metadata_values_to_string:
for k in expected_metadata:
v = expected_metadata[k]
if isinstance(v, list):
v = [str(i) for i in v]
elif isinstance(v, tuple):
v = (str(i) for i in v)
else:
v = str(v)
expected_metadata[k] = v
for k in item_annotations_as_dict:
v = item_annotations_as_dict[k]
if isinstance(v, list):
v = [str(i) for i in v]
elif isinstance(v, tuple):
v = (str(i) for i in v)
else:
v = str(v)
item_annotations_as_dict[k] = v
# # for annote in item.annotations:
# # print("{}: {}".format(annote.name, annote.value))
# # k1 = sorted(list(item_annotations_as_dict.keys()))
# # k2 = sorted(list(expected_metadata.keys()))
# # print("--")
# # for k in k1:
# # print("'{}':'{}'".format(k, item_annotations_as_dict[k]))
# # print("--")
# # for k in k2:
# # print("'{}':'{}'".format(k, expected_metadata[k]))
# # self.assertEqual(len(k1), len(k2))
# # self.assertEqual(set(k1), set(k2))
# for key in set(item_annotations_as_dict.keys()):
# if item_annotations_as_dict[key] != expected_metadata[key]:
# v = expected_metadata[key]
# # if isinstance(v, list):
# # print("{}: {}".format(v, [type(i) for i in v]))
# # elif isinstance(v, tuple):
# # print("{}: {}".format(v, (type(i) for i in v)))
# # else:
# # print("{}: {}".format(v, type(v)))
# print("**** {}:\t\t{} ({}) \t\t{} ({})".format(
# key,
# item_annotations_as_dict[key],
# type(item_annotations_as_dict[key]),
# expected_metadata[key],
# type(expected_metadata[key]),
# ))
self.assertEqual(item_annotations_as_dict, expected_metadata)
def check_metadata_annotations(self,
item,
reference):
expected_annotations = reference["metadata"]
self.compare_annotations_to_json_metadata_dict(item, expected_annotations)
def check_comments(self, item, reference):
reference_comments = list(reference["comments"])
item_comments = list(item.comments)
self.assertEqualUnorderedSequences(item_comments, reference_comments)
def compare_to_reference_by_title_and_index(self,
tree,
tree_file_title,
reference_tree_idx):
ref_tree = self.tree_references[tree_file_title][str(reference_tree_idx)]
self.compare_to_reference_tree(tree, ref_tree)
def compare_to_reference_tree(self, tree, ref_tree):
self.assertIs(tree.is_rooted, ref_tree["is_rooted"])
if self.__class__.is_check_comments:
self.check_comments(tree, ref_tree)
self.check_metadata_annotations(
item=tree,
reference=ref_tree)
obs_taxon_labels = []
obs_node_labels = []
obs_edge_labels = []
visited_nodes = []
self.preprocess_tree_to_be_checked(tree)
for node_idx, node in enumerate(tree):
visited_nodes.append(node)
ref_node = ref_tree["nodes"][node.label]
ref_node_label = ref_node["label"]
ref_node_taxon_label = ref_node["taxon_label"]
self.assertEqual(node.label, ref_node_label)
ref_node_children = ref_node["children"]
self.assertEqual(len(node._child_nodes), len(ref_node_children))
if node.taxon:
self.assertEqual(node.taxon.label, ref_node_taxon_label)
obs_taxon_labels.append(node.taxon.label)
else:
self.assertEqual(ref_node_taxon_label, None)
obs_node_labels.append(node.label)
if ref_node_children:
self.assertTrue(node.is_internal())
self.assertFalse(node.is_leaf())
else:
self.assertFalse(node.is_internal())
self.assertTrue(node.is_leaf())
if node.parent_node is None:
self.assertEqual(ref_node["parent"], None)
else:
self.assertEqual(node.parent_node.label, ref_node["parent"])
if node.parent_node.taxon:
self.assertEqual(node.parent_node.taxon.label, ref_node["parent"])
child_labels = [ch.label for ch in node.child_node_iter()]
self.assertEqual(len(child_labels), len(ref_node["children"]))
self.assertEqual(set(child_labels), set(ref_node["children"]))
edge = node.edge
ref_edge = ref_tree["edges"][edge.label]
if edge.tail_node is None:
self.assertEqual(ref_edge["tail_node"], None)
else:
self.assertEqual(edge.tail_node.label, ref_edge["tail_node"])
self.assertEqual(edge.head_node.label, ref_edge["head_node"])
self.assertAlmostEqual(node.edge.length, float(ref_edge["length"]), 3)
def compare_to_reference_by_title_and_index2(self,
tree,
tree_file_title,
reference_tree_idx,
suppress_internal_node_taxa,
suppress_leaf_node_taxa,
is_metadata_extracted,
is_coerce_metadata_values_to_string,
is_distinct_nodes_and_edges_representation,
is_taxa_managed_separately_from_tree):
ref_tree = self.tree_references[tree_file_title][str(reference_tree_idx)]
self.assertIs(tree.is_rooted, ref_tree["is_rooted"])
self.check_comments(
tree,
ref_tree)
self.check_metadata_annotations(
item=tree,
reference=ref_tree,
is_coerce_metadata_values_to_string=False)
obs_taxa = []
obs_node_labels = []
obs_edge_labels = []
visited_nodes = []
for node in tree:
if node.taxon is not None:
node.canonical_label = node.taxon.label
else:
node.canonical_label = node.label
for node_idx, node in enumerate(tree):
visited_nodes.append(node)
ref_node = ref_tree["nodes"][node.label]
ref_node_label = ref_node["label"]
self.assertEqual(node.label, ref_node_label)
ref_edge = ref_tree["edges"][node.edge.label]
self.assertEqual(node.edge.label, ref_edge["label"])
ref_node_children = ref_node["children"]
if ref_node_children:
self.assertTrue(node.is_internal())
self.assertFalse(node.is_leaf())
self.assertEqual(len(node._child_nodes), len(ref_node_children))
if suppress_internal_node_taxa:
self.assertEqual(node.label, ref_node_label)
self.assertIs(node.taxon, None)
obs_node_labels.append(node.label)
else:
if not self.__class__.is_distinct_taxa_and_labels_on_tree:
self.assertIsNot(node.taxon, None)
self.assertEqual(node.taxon.label, ref_node_label)
self.assertIs(ch.label, None)
obs_taxa.append(node.taxon)
else:
obs_taxa.append(node.label)
obs_node_labels.append(node.label)
else:
self.assertFalse(node.is_internal())
self.assertTrue(node.is_leaf())
self.assertEqual(len(node._child_nodes), len(ref_node_children))
if suppress_leaf_node_taxa:
self.assertEqual(node.label, ref_node_label)
self.assertIs(node.taxon, None)
obs_node_labels.append(node.label)
else:
self.assertIsNot(node.taxon, None)
self.assertEqual(node.taxon.label, ref_node_label)
if not self.__class__.is_distinct_taxa_and_labels_on_tree:
self.assertIs(ch.label, None)
obs_taxa.append(node.taxon)
if node.parent_node is not None:
if node.parent_node.is_internal:
if suppress_internal_node_taxa:
self.assertEqual(node.parent_node.label, ref_node["parent"])
self.assertIs(node.parent_node.taxon, None)
else:
if not self.__class__.is_distinct_taxa_and_labels_on_tree:
self.assertEqual(node.parent_node.taxon.label, ref_node["parent"])
self.assertIs(node.parent_node.label, None)
else:
self.assertEqual(node.parent_node.label, ref_node["parent"])
else:
if suppress_leaf_node_taxa:
self.assertEqual(node.parent_node.label, ref_node["parent"])
self.assertIs(node.parent_node.taxon, None)
else:
self.assertEqual(node.parent_node.taxon.label, ref_node["parent"])
self.assertIs(node.parent_node.label, None)
else:
self.assertEqual(ref_node["parent"], "None")
child_labels = []
for ch in node.child_node_iter():
if ch.is_internal():
if suppress_internal_node_taxa:
self.assertIs(ch.taxon, None)
child_labels.append(ch.label)
else:
if not self.__class__.is_distinct_taxa_and_labels_on_tree:
self.assertIsNot(ch.taxon, None)
child_labels.append(ch.taxon.label)
self.assertIs(ch.label, None)
else:
self.assertEqual(node.label, ref_node_label)
child_labels.append(ch.label)
else:
if suppress_leaf_node_taxa:
self.assertIs(ch.taxon, None)
child_labels.append(ch.label)
else:
self.assertIsNot(ch.taxon, None)
child_labels.append(ch.taxon.label)
if not self.__class__.is_distinct_taxa_and_labels_on_tree:
self.assertIs(ch.label, None)
self.assertEqual(len(child_labels), len(ref_node["children"]))
self.assertEqual(set(child_labels), set(ref_node["children"]))
edge = node.edge
ref_edge = ref_tree["edges"][node.canonical_label]
if edge.tail_node is None:
self.assertEqual(ref_edge["tail_node"], "None")
else:
self.assertEqual(edge.tail_node.canonical_label, ref_edge["tail_node"])
self.assertEqual(edge.head_node.canonical_label, ref_edge["head_node"])
self.assertAlmostEqual(node.edge.length, float(ref_edge["length"]), 3)
# This hackery because NEWICK/NEXUS cannot distinguish between
# node and edge comments, and everything gets lumped in as a
# node comment
if not is_distinct_nodes_and_edges_representation:
node.comments += edge.comments
d = {
"comments": ref_node["comments"] + ref_edge["comments"],
"metadata_comments": ref_node["metadata_comments"] + ref_edge["metadata_comments"],
}
self.check_comments(node, d, is_metadata_extracted)
if is_metadata_extracted:
obs_tuples = []
for o in (node, edge):
for a in o.annotations:
# print("++ {}: {} = {} ({})".format(type(o), a.name, a.value, type(a.value)))
v = a.value
if isinstance(v, list):
v = tuple(v)
obs_tuples.append( (a.name, v) )
exp_tuples = []
for idx, o in enumerate((ref_node["metadata"], ref_edge["metadata"])):
for k in o:
v = o[k]
# print("-- {}{}: {} = {}".format(type(o), idx+1, k, v))
if isinstance(v, list):
if is_coerce_metadata_values_to_string:
v = tuple(str(vx) for vx in v)
else:
v = tuple(v)
elif is_coerce_metadata_values_to_string:
v = str(v)
# print("-- {}{}: {} = {} ({})".format(type(o), idx+1, k, v, type(v)))
exp_tuples.append( (k, v) )
self.assertEqualUnorderedSequences(tuple(obs_tuples), tuple(exp_tuples))
else:
if self.__class__.is_check_comments:
self.check_comments(node, ref_node, is_metadata_extracted)
self.check_comments(edge, ref_edge, is_metadata_extracted)
if self.__class__.is_metadata_extracted:
self.check_metadata_annotations(
item=node,
reference=ref_node,
is_coerce_metadata_values_to_string=is_coerce_metadata_values_to_string)
self.check_metadata_annotations(
item=edge,
reference=ref_edge,
is_coerce_metadata_values_to_string=is_coerce_metadata_values_to_string)
self.assertEqual(len(visited_nodes), len(ref_tree["nodeset"]))
if self.__class__.is_taxa_managed_separately_from_tree:
self.assertEqual(len(obs_taxa), len(tree.taxon_namespace))
self.assertEqual(set(obs_taxa), set(tree.taxon_namespace))
obs_node_labels.extend([t.label for t in tree.taxon_namespace])
elif not self.__class__.is_distinct_taxa_and_labels_on_tree:
# node labels may have been interpreted as taxa depending on read mode
obs_node_labels.extend([t.label for t in tree.taxon_namespace if t.label not in obs_node_labels])
self.assertEqual(len(obs_node_labels), len(ref_tree["nodeset"]))
self.assertEqual(set(obs_node_labels), set(ref_tree["nodeset"]))
def verify_standard_trees(self,
tree_list,
tree_file_title,
tree_offset=0):
tree_reference = self.tree_references[tree_file_title]
expected_number_of_trees = tree_reference["num_trees"]
if tree_offset < 0:
if abs(tree_offset) > expected_number_of_trees:
tree_offset = 0
else:
tree_offset = expected_number_of_trees + tree_offset
self.assertEqual(len(tree_list), expected_number_of_trees-tree_offset)
# for tree_idx, (tree, ref_tree) in enumerate(zip(tree_list, tree_directory[tree_file_title])):
for tree_idx, tree in enumerate(tree_list):
_LOG.debug("{}: {}".format(tree_file_title, tree_idx))
self.assertIs(tree.taxon_namespace, tree_list.taxon_namespace)
self.compare_to_reference_by_title_and_index(
tree=tree,
tree_file_title=tree_file_title,
reference_tree_idx=tree_idx + tree_offset)
class NewickTestTreesChecker(StandardTestTreesChecker):
@staticmethod
def create_class_fixtures(cls,
schema="newick",
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
is_metadata_extracted=False,
is_coerce_metadata_values_to_string=True,
is_taxa_managed_separately_from_tree=False,
is_check_comments=True):
cls.schema = schema
cls.schema_tree_filepaths = copy.deepcopy(_TREE_FILEPATHS[cls.schema])
cls.tree_references = copy.deepcopy(_TREE_REFERENCES)
for tree_file_title in cls.tree_references:
for reference_tree_idx in range(cls.tree_references[tree_file_title]["num_trees"]):
ref_tree = cls.tree_references[tree_file_title][str(reference_tree_idx)]
for ref_node_label in ref_tree["nodes"]:
ref_node = ref_tree["nodes"][ref_node_label]
ref_node_taxon_label = ref_node["taxon_label"]
if ref_node["children"]:
if suppress_internal_node_taxa and ref_node["taxon_label"]:
ref_node["taxon_label"] = None
elif not suppress_internal_node_taxa and ref_node["taxon_label"] is None:
ref_node["taxon_label"] = ref_node["label"]
if not ref_node["children"]:
ref_node["taxon_label"] = None
if suppress_leaf_node_taxa and ref_node["taxon_label"]:
ref_node["taxon_label"] = None
elif not suppress_leaf_node_taxa and ref_node["taxon_label"] is None:
ref_node["taxon_label"] = ref_node["label"]
for ref_edge_label in ref_tree["edges"]:
ref_edge = ref_tree["edges"][ref_edge_label]
ref_edge["label"] = "None"
cls.suppress_internal_node_taxa = suppress_internal_node_taxa
cls.suppress_leaf_node_taxa = suppress_leaf_node_taxa
cls.is_metadata_extracted = is_metadata_extracted
cls.is_coerce_metadata_values_to_string = is_coerce_metadata_values_to_string
cls.is_taxa_managed_separately_from_tree = is_taxa_managed_separately_from_tree
cls.is_check_comments = is_check_comments
def preprocess_tree_to_be_checked(self, tree):
for nd in tree:
if nd.is_internal():
if self.__class__.suppress_internal_node_taxa:
self.assertIs(nd.taxon, None)
else:
self.assertIsNot(nd.taxon, None)
else:
if self.__class__.suppress_leaf_node_taxa:
self.assertIs(nd.taxon, None)
else:
self.assertIsNot(nd.taxon, None)
if nd.taxon is not None:
nd.label = nd.taxon.label
nd.edge.label = nd.label
class NexusTestTreesChecker(NewickTestTreesChecker):
@staticmethod
def create_class_fixtures(cls,
schema="nexus",
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
is_metadata_extracted=True,
is_coerce_metadata_values_to_string=True,
is_taxa_managed_separately_from_tree=True,
is_check_comments=True):
NewickTestTreesChecker.create_class_fixtures(cls,
schema=schema,
suppress_internal_node_taxa=suppress_internal_node_taxa,
suppress_leaf_node_taxa=suppress_leaf_node_taxa,
is_metadata_extracted=is_metadata_extracted,
is_coerce_metadata_values_to_string=is_coerce_metadata_values_to_string,
is_taxa_managed_separately_from_tree=is_taxa_managed_separately_from_tree,
is_check_comments=is_check_comments)
class NexmlTestTreesChecker(StandardTestTreesChecker):
@staticmethod
def create_class_fixtures(cls):
cls.schema = "nexml"
cls.schema_tree_filepaths = copy.deepcopy(_TREE_FILEPATHS[cls.schema])
cls.tree_references = copy.deepcopy(_TREE_REFERENCES)
cls.is_coerce_metadata_values_to_string = False
cls.is_taxa_managed_separately_from_tree = True
cls.is_check_comments = False
|
