def test_midpoint_root(self):
unrooted_nwk = io.StringIO("((a:1,b:1):1,(c:5,d:4):1);")
rooted_nwk = io.StringIO("(c:4.5,(d:4,(a:1,b:1):2):0.5);")
unrooted_tree = skbio.TreeNode.read(unrooted_nwk)
expected = skbio.TreeNode.read(rooted_nwk)
actual = midpoint_root(unrooted_tree)
# skbio.TreeNode currently does not have an equality operator
# (see https://github.com/biocore/scikit-bio/issues/465), so do a
# few specific comparisons of actual and expected
# confirm ids are as expected
actual_tip_tip_distances = actual.tip_tip_distances()
expected_tip_tip_distances = expected.tip_tip_distances()
self.assertEqual(sorted(actual_tip_tip_distances.ids),
sorted(expected_tip_tip_distances.ids))
# confirm tip-to-tip distances are as expected
for id1 in actual_tip_tip_distances.ids:
for id2 in actual_tip_tip_distances.ids:
actual_distance = actual_tip_tip_distances[id1, id2]
expected_distance = expected_tip_tip_distances[id1, id2]
self.assertEqual(
actual_distance, expected_distance,
"Distances between %s and %s are not equal. (%f versus %f)."
% (id1, id2, actual_distance, expected_distance))
# confirm tip-to-root distances are as expected
for id_ in actual_tip_tip_distances.ids:
self.assertEqual(
actual.find(id_).distance(actual.root()),
expected.find(id_).distance(expected.root()))
def test_midpoint_root(self):
unrooted_nwk = io.StringIO("((a:1,b:1):1,(c:5,d:4):1);")
rooted_nwk = io.StringIO("(c:4.5,(d:4,(a:1,b:1):2):0.5);")
unrooted_tree = skbio.TreeNode.read(unrooted_nwk)
expected = skbio.TreeNode.read(rooted_nwk)
actual = midpoint_root(unrooted_tree)
# skbio.TreeNode currently does not have an equality operator
# (see https://github.com/biocore/scikit-bio/issues/465), so do a
# few specific comparisons of actual and expected
# confirm ids are as expected
actual_tip_tip_distances = actual.tip_tip_distances()
expected_tip_tip_distances = expected.tip_tip_distances()
self.assertEqual(sorted(actual_tip_tip_distances.ids),
sorted(expected_tip_tip_distances.ids))
# confirm tip-to-tip distances are as expected
for id1 in actual_tip_tip_distances.ids:
for id2 in actual_tip_tip_distances.ids:
actual_distance = actual_tip_tip_distances[id1, id2]
expected_distance = expected_tip_tip_distances[id1, id2]
self.assertEqual(
actual_distance, expected_distance,
"Distances between %s and %s are not equal. (%f versus %f)." %
(id1, id2, actual_distance, expected_distance))
# confirm tip-to-root distances are as expected
for id_ in actual_tip_tip_distances.ids:
self.assertEqual(actual.find(id_).distance(actual.root()),
expected.find(id_).distance(expected.root()))