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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 dendropy
from dendropy.test.support import standard_file_test_trees
class NewickTreeListReaderTaxaManagementBaseTestCase(standard_file_test_trees.NewickTestTreesChecker):
def test_get(self):
tree_file_title = "dendropy-test-trees-n12-x2"
tree_filepath = self.schema_tree_filepaths[tree_file_title]
kwargs = {
"suppress_internal_node_taxa": self.__class__.suppress_internal_node_taxa,
"suppress_leaf_node_taxa": self.__class__.suppress_leaf_node_taxa,
}
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:
tree_list = method(src,
self.__class__.schema,
**kwargs)
self.verify_standard_trees(
tree_list=tree_list,
tree_file_title=tree_file_title)
def test_selective_taxa_read(self):
tree_file_title = "dendropy-test-trees-n12-x2"
tree_filepath = self.schema_tree_filepaths[tree_file_title]
kwargs = {
"suppress_internal_node_taxa": self.__class__.suppress_internal_node_taxa,
"suppress_leaf_node_taxa": self.__class__.suppress_leaf_node_taxa,
}
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()
old_id = id(tree_list)
f = getattr(tree_list, method)
f(src, self.__class__.schema, **kwargs)
new_id = id(tree_list)
self.verify_standard_trees(
tree_list=tree_list,
tree_file_title=tree_file_title)
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