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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.
##
##############################################################################
"""
NEXUS data read/write parse/format tests.
"""
import unittest
from dendropy.test.support import pathmap
from dendropy.utility.messaging import get_logger
from dendropy.calculate import treecompare
import dendropy
_LOG = get_logger(__name__)
class TreeFromBipartitionsTest(unittest.TestCase):
def testTrees(self):
tree_files = [
("dendropy-test-trees-n33-unrooted-x100a.nexus", "force-unrooted", False),
("dendropy-test-trees-multifurcating-unrooted.nexus", "force-unrooted", False),
("pythonidae.beast.summary.tre", "force-rooted", True),
("primates.beast.mcct.medianh.tre", "force-rooted", True),
]
for tree_file, rooting, is_rooted in tree_files:
ref_tree = dendropy.Tree.get_from_path(pathmap.tree_source_path(tree_file),
"nexus",
rooting=rooting)
bipartition_encoding = ref_tree.encode_bipartitions()
t_tree = dendropy.Tree.from_bipartition_encoding(
bipartition_encoding,
taxon_namespace=ref_tree.taxon_namespace,
is_rooted=ref_tree.is_rooted)
# t_tree.encode_bipartitions()
_LOG.debug("--\n File: {} ({})".format(tree_file, ref_tree.is_rooted))
_LOG.debug(" Original: {}".format(ref_tree.as_string("newick")))
_LOG.debug("Reconstructed: {}".format(t_tree.as_string("newick")))
self.assertEqual(treecompare.symmetric_difference(ref_tree, t_tree), 0)
if __name__ == "__main__":
unittest.main()
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