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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 NeXML tree writing.
"""
import collections
import unittest
import dendropy
import re
from dendropy.test.support import pathmap
from dendropy.test.support import compare_and_validate
from dendropy.test.support import dendropytest
from dendropy.test.support import curated_test_tree
from dendropy.test.support import standard_file_test_trees
class NexmlTreeWriterTests(
curated_test_tree.CuratedTestTree,
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
def test_simple(self):
tree1, all_nodes, leaf_nodes, internal_nodes = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False
)
s = tree1.as_string("nexml")
tree2 = dendropy.Tree.get_from_string(
s, "nexml",
)
self.verify_curated_tree(tree2)
class NexmlTreeWriterDefaultTest(
standard_file_test_trees.NexmlTestTreesChecker,
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NexmlTestTreesChecker.create_class_fixtures(cls)
def test_roundtrip_full(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-annotated-x10a'
tree_filepath = standard_file_test_trees._TREE_FILEPATHS["nexml"][tree_file_title]
tree1 = dendropy.Tree.get_from_path(
tree_filepath,
"nexml",
)
s = tree1.as_string("nexml")
tree2 = dendropy.Tree.get_from_string(
s,
"nexml",
)
self.compare_to_reference_by_title_and_index(
tree=tree2,
tree_file_title=tree_file_title,
reference_tree_idx=0)
class NexmlStandardTreeListWriterTestCase(
compare_and_validate.ValidateWriteable,
standard_file_test_trees.NexmlTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NexmlTestTreesChecker.create_class_fixtures(cls)
def test_annotated_tree_list_writing(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-annotated-x10a'
tree_filepath = self.schema_tree_filepaths[tree_file_title]
tree_list1 = dendropy.TreeList.get_from_path(
tree_filepath,
"nexml")
s = self.write_out_validate_equal_and_return(
tree_list1, "nexml", {})
tree_list2 = dendropy.TreeList.get_from_string(s,
"nexml")
self.verify_standard_trees(
tree_list=tree_list2,
tree_file_title=tree_file_title,
tree_offset=0)
if __name__ == "__main__":
unittest.main()
|
