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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 unittest
from dendropy.test.support import pathmap
import dendropy
class TreeArrayBasicTreeAccession(unittest.TestCase):
def get_trees(self, taxon_namespace=None):
trees = dendropy.TreeList.get_from_path(pathmap.tree_source_path(
"pythonidae.reference-trees.nexus"),
"nexus",
taxon_namespace=taxon_namespace)
return trees
def verify_tree_array(self, tree_array, source_trees, ignore_edges=False):
self.assertEqual(len(tree_array), len(source_trees))
for idx, source_tree in enumerate(source_trees):
source_splits = [b.split_bitmask for b in source_tree.encode_bipartitions()]
tss_splits, tss_edges = tree_array.get_split_bitmask_and_edge_tuple(idx)
self.assertEqual(len(tss_splits), len(source_splits))
self.assertEqual(set(tss_splits), set(source_splits))
# since encoding is done in postorder, we can rely on correspondence of index ...
for idx, nd in enumerate(source_tree.postorder_node_iter()):
source_split = nd.edge.bipartition.split_bitmask
tss_split = tss_splits[idx]
tss_edge_length = tss_edges[idx]
self.assertEqual(source_split, tss_split)
if nd.edge.length is None:
self.assertEqual(tss_edge_length, 0)
else:
self.assertAlmostEqual(tss_edge_length, nd.edge.length)
def test_add_tree(self):
trees = self.get_trees()
tree_array = dendropy.TreeArray(taxon_namespace=trees.taxon_namespace)
for tree in trees:
tree_array.add_tree(tree)
self.verify_tree_array(tree_array, trees)
if __name__ == "__main__":
unittest.main()
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