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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 random
import dendropy
from dendropy.test.support import standard_file_test_trees
class StandardTreesParsingTestCase(standard_file_test_trees.StandardTestTreesChecker):
def test_default_get(self):
for tree_file_title in [
"dendropy-test-trees-multifurcating-rooted",
"dendropy-test-trees-multifurcating-unrooted",
"dendropy-test-trees-n10-rooted-treeshapes",
"dendropy-test-trees-n14-unrooted-treeshapes",
]:
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
{"path": tree_filepath},
{"file": tree_stream},
{"data": tree_string},
)
for approach_kwargs in approaches:
approach_kwargs["schema"] = self.__class__.schema
tree_list = dendropy.TreeList.get(**approach_kwargs)
self.verify_standard_trees(tree_list=tree_list,
tree_file_title=tree_file_title)
def test_default_read(self):
preloaded_tree_file_title = "dendropy-test-trees-n33-unrooted-x10a"
preloaded_tree_reference = self.tree_references[preloaded_tree_file_title]
tree_file_title = "dendropy-test-trees-n33-unrooted-x10a"
tree_reference = self.tree_references[tree_file_title]
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
{"path": tree_filepath},
{"file": tree_stream},
{"data": tree_string},
)
for approach_kwargs in approaches:
# prepopulate
tree_list = dendropy.TreeList.get(
path=self.schema_tree_filepaths[preloaded_tree_file_title],
schema=self.__class__.schema)
# check to make sure trees were loaded
old_len = len(tree_list)
self.assertEqual(old_len, len(tree_list._trees))
self.assertEqual(old_len, preloaded_tree_reference["num_trees"])
self.verify_standard_trees(tree_list, preloaded_tree_file_title)
# load
old_id = id(tree_list)
approach_kwargs["schema"] = self.__class__.schema
trees_read = tree_list.read(**approach_kwargs)
new_id = id(tree_list)
self.assertEqual(old_id, new_id)
# make sure new trees added
new_len = len(tree_list)
self.assertEqual(new_len, len(tree_list._trees))
expected_number_of_trees = tree_reference["num_trees"]
self.assertEqual(old_len + expected_number_of_trees, new_len)
self.assertEqual(trees_read, expected_number_of_trees)
# check new trees
for tree_idx, tree in enumerate(tree_list[old_len:]):
self.compare_to_reference_by_title_and_index(
tree=tree,
tree_file_title=tree_file_title,
reference_tree_idx=tree_idx)
# make sure old ones still intact
for tree_idx, tree in enumerate(tree_list[:old_len]):
self.compare_to_reference_by_title_and_index(
tree=tree,
tree_file_title=preloaded_tree_file_title,
reference_tree_idx=tree_idx)
def test_tree_offset_get(self):
tree_file_title = "dendropy-test-trees-n33-unrooted-x100a"
tree_reference = self.tree_references[tree_file_title]
expected_number_of_trees = tree_reference["num_trees"]
tree_offsets = set([0, expected_number_of_trees-1, -1, -expected_number_of_trees])
while len(tree_offsets) < 8:
tree_offsets.add(random.randint(1, expected_number_of_trees-2))
while len(tree_offsets) < 12:
tree_offsets.add(random.randint(-expected_number_of_trees-2, -2))
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
for tree_offset in tree_offsets:
with open(tree_filepath, "r") as tree_stream:
approaches = (
(dendropy.TreeList.get_from_path, tree_filepath),
(dendropy.TreeList.get_from_stream, tree_stream),
(dendropy.TreeList.get_from_string, tree_string),
)
for method, src in approaches:
tree_list = method(
src,
self.__class__.schema,
collection_offset=0,
tree_offset=tree_offset)
self.verify_standard_trees(
tree_list=tree_list,
tree_file_title=tree_file_title,
tree_offset=tree_offset)
def test_tree_offset_read(self):
tree_file_title = "dendropy-test-trees-n33-unrooted-x100a"
tree_reference = self.tree_references[tree_file_title]
expected_number_of_trees = tree_reference["num_trees"]
tree_offsets = set([0, expected_number_of_trees-1, -1, -expected_number_of_trees])
while len(tree_offsets) < 8:
tree_offsets.add(random.randint(1, expected_number_of_trees-2))
while len(tree_offsets) < 12:
tree_offsets.add(random.randint(-expected_number_of_trees-2, -2))
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
for tree_offset in tree_offsets:
with open(tree_filepath, "r") as tree_stream:
approaches = (
("read_from_path", tree_filepath),
("read_from_stream", tree_stream),
("read_from_string", tree_string),
)
for method, src in approaches:
tree_list = dendropy.TreeList()
f = getattr(tree_list, method)
trees_read = f(src,
self.__class__.schema,
# collection_offset=0,
tree_offset=tree_offset)
self.verify_standard_trees(
tree_list=tree_list,
tree_file_title=tree_file_title,
tree_offset=tree_offset)
def test_out_of_range_tree_offset_get(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-x10a'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
tree_reference = self.tree_references[tree_file_title]
expected_number_of_trees = tree_reference["num_trees"]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
(dendropy.TreeList.get_from_path, tree_filepath),
(dendropy.TreeList.get_from_stream, tree_stream),
(dendropy.TreeList.get_from_string, tree_string),
)
for method, src in approaches:
with self.assertRaises(IndexError):
method(src, self.__class__.schema, collection_offset=0, tree_offset=expected_number_of_trees)
def test_out_of_range_tree_offset_read(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-x10a'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
tree_reference = self.tree_references[tree_file_title]
expected_number_of_trees = tree_reference["num_trees"]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
("read_from_path", tree_filepath),
("read_from_stream", tree_stream),
("read_from_string", tree_string),
)
for method, src in approaches:
tree_list = dendropy.TreeList()
f = getattr(tree_list, method)
with self.assertRaises(IndexError):
f(src, self.__class__.schema, collection_offset=0, tree_offset=expected_number_of_trees)
def test_out_of_range_collection_offset_get(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-x10a'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
(dendropy.TreeList.get_from_path, tree_filepath),
(dendropy.TreeList.get_from_stream, tree_stream),
(dendropy.TreeList.get_from_string, tree_string),
)
for method, src in approaches:
with self.assertRaises(IndexError):
method(src, self.__class__.schema, collection_offset=1, tree_offset=0)
def test_out_of_range_collection_offset_read(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-x10a'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
("read_from_path", tree_filepath),
("read_from_stream", tree_stream),
("read_from_string", tree_string),
)
for method, src in approaches:
tree_list = dendropy.TreeList()
f = getattr(tree_list, method)
with self.assertRaises(IndexError):
f(src, self.__class__.schema, collection_offset=1, tree_offset=0)
def test_unsupported_keyword_arguments_get(self):
tree_file_title = 'dendropy-test-trees-n12-x2'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
(dendropy.TreeList.get_from_path, tree_filepath),
(dendropy.TreeList.get_from_stream, tree_stream),
(dendropy.TreeList.get_from_string, tree_string),
)
for method, src in approaches:
with self.assertRaises(TypeError):
method(src,
self.__class__.schema,
suppress_internal_taxa=True, # should be suppress_internal_node_taxa
gobbledegook=False,
)
def test_unsupported_keyword_arguments_read(self):
tree_file_title = 'dendropy-test-trees-n12-x2'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
("read_from_path", tree_filepath),
("read_from_stream", tree_stream),
("read_from_string", tree_string),
)
for method, src in approaches:
tree_list = dendropy.TreeList()
f = getattr(tree_list, method)
with self.assertRaises(TypeError):
f(src,
self.__class__.schema,
suppress_internal_taxa=True, # should be suppress_internal_node_taxa
gobbledegook=False,
)
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