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|
import pathlib
import pytest
from cogent3 import make_tree
from cogent3.phylo.tree_distance import (
lin_rajan_moret,
matching_cluster_distance,
rooted_robinson_foulds,
unrooted_robinson_foulds,
)
ROOTED_DISTANCE_MEASURES = matching_cluster_distance, rooted_robinson_foulds
UNROOTED_DISTANCE_MEASURES = lin_rajan_moret, unrooted_robinson_foulds
# unrooted rf distance
def test_unrooted_rf_different_trees():
a = make_tree(treestring="(a, b, (c, (d, e)));")
# There are two splits not in common for the two trees
# abc-de in tree a, and ad-dce in tree b.
b = make_tree(treestring="(a, b, (d, (c, e)));")
distance = unrooted_robinson_foulds(a, b)
assert distance == 2
distance = unrooted_robinson_foulds(b, a)
assert distance == 2
# Identical unrooted tree as before, but a different orientation.
b = make_tree(treestring="((a, b), d, (c, e));")
distance = unrooted_robinson_foulds(a, b)
assert distance == 2
distance = unrooted_robinson_foulds(b, a)
assert distance == 2
# Identical unrooted tree as before, but a different orientation.
b = make_tree(treestring="(((a, b), d), c, e);")
distance = unrooted_robinson_foulds(a, b)
assert distance == 2
distance = unrooted_robinson_foulds(b, a)
assert distance == 2
a = make_tree(treestring="(a, (b, (c, d)), (e, (f, (g, h))));")
b = make_tree(treestring="(a, (c, (b, d)), (h, (f, (g, e))));")
# There are six splits not in common.
# For tree a they are cd-abefgh, abcdef-gh, and abcde-fgh
# For tree b they are bd-acefgh, abcdhf-ge, and abcdh-fge
distance = unrooted_robinson_foulds(a, b)
assert distance == 6
distance = unrooted_robinson_foulds(b, a)
assert distance == 6
def test_unrooted_rf_same_tree():
# Topology of the unrooted trees are identical
# though they are stored in different orientations.
a = make_tree(treestring="(a, b, (c, d));")
b = make_tree(treestring="(c, d, (a, b));")
distance = unrooted_robinson_foulds(a, b)
assert distance == 0
distance = unrooted_robinson_foulds(b, a)
assert distance == 0
def test_unrooted_rf_distance_multifurcation():
a = make_tree(treestring="(a, b, (c, (d, e)));")
b = make_tree(treestring="(a, b, (c, d, e));")
# There is one split not in common.
# Tree a: abc-de
distance = unrooted_robinson_foulds(a, b)
assert distance == 1
distance = unrooted_robinson_foulds(b, a)
assert distance == 1
a = make_tree(treestring="(a, b, (((c1, c2), (d1, (d2, d3))), (e1, (e2, e3))));")
b = make_tree(treestring="(a, b, ((c1, c2), (d2, (d1, d3)), (e1, e2, e3)));")
# There are four splits not in common
# Tree a: e1-others, d2,d3-others, c's and d's - others
# Tree b: d1,d3-others
distance = unrooted_robinson_foulds(a, b)
assert distance == 4
distance = unrooted_robinson_foulds(b, a)
assert distance == 4
# lin_rajan_moret distance
def test_lrm_different_trees():
a = make_tree(treestring="(1,(((2,3),4),(5,((6,(7,(8,9))),(10,11)))),12);")
b = make_tree(treestring="(1,((((2,3),4),5),((6,7),((8,9),(10,11)))),12);")
distance = lin_rajan_moret(a, b)
assert distance == 8
def test_lrm_matches_original_implementation_small_tree(DATA_DIR):
path, expect = DATA_DIR / "match_dist_100.tree", 1402
data = path.read_text().splitlines()
t1 = make_tree(data[0])
t2 = make_tree(data[1])
distance = lin_rajan_moret(t1, t2)
# Assert that this is same value as original C implementation
assert distance == expect
@pytest.mark.slow
def test_lrm_matches_original_implementation_big_tree(DATA_DIR):
path, expect = DATA_DIR / "match_dist_2000.tree", 17037
data = pathlib.Path(path).read_text().splitlines()
t1 = make_tree(data[0])
t2 = make_tree(data[1])
distance = lin_rajan_moret(t1, t2)
# Assert that this is same value as original C implementation
assert distance == expect
def test_lrm_same_tree():
# Topology of the unrooted trees are identical
# though they are stored in different orientations.
a = make_tree(treestring="(a, b, (c, d));")
b = make_tree(treestring="(c, d, (a, b));")
distance = lin_rajan_moret(a, b)
assert distance == 0
distance = lin_rajan_moret(b, a)
assert distance == 0
# rooted rf distance
def test_rooted_rf_multifurcation():
a = make_tree(treestring="((a, b), (c, d));")
b = make_tree(treestring="((a, c, b), d);")
# There are three clades not in common
# Tree a: ab, cd
# Tree b: acb
distance = rooted_robinson_foulds(a, b)
assert distance == 3
distance = rooted_robinson_foulds(b, a)
assert distance == 3
def test_rooted_rf_different_trees():
a = make_tree(
treestring="((((a1,a2),(b1,b2,b3),x),(c1,c2,c3),(d1,d2)),(e1,(e2,e3)));"
)
b = make_tree(
treestring="((((a1,a2),(b1,b2,b3)),x,(c1,c2,c3),(d1,d2)),(e1,(e2,e3)));"
)
# Moving the single x up one level creates two clades that are not in common.
# Tree a: ABx
# Tree b: AB
distance = rooted_robinson_foulds(a, b)
assert distance == 2
distance = rooted_robinson_foulds(b, a)
assert distance == 2
a = make_tree(treestring="((a,b),c);")
b = make_tree(treestring="((a,c),b);")
# There are two clades not in common
# Tree a: ab
# Tree b: ac
distance = rooted_robinson_foulds(a, b)
assert distance == 2
distance = rooted_robinson_foulds(b, a)
assert distance == 2
a = make_tree(treestring="((a,(b1,(b2,b3))),((c1,c2),(c3,c4)));")
b = make_tree(treestring="((a,((c1,c2),(c3,c4))),(b1,(b2,b3)));")
# There are two clades not in common
# Tree a: aB
# Tree b: aC
distance = rooted_robinson_foulds(a, b)
assert distance == 2
distance = rooted_robinson_foulds(b, a)
assert distance == 2
a = make_tree(treestring="(a,(b,(c,(d,(e,f)))));")
b = make_tree(treestring="(a,(f,(c,(d,(b,e)))));")
# There are six clades not in common
# Tree a: ef, def, cdef
# Tree b: be, bde, bcde
distance = rooted_robinson_foulds(a, b)
assert distance == 6
distance = rooted_robinson_foulds(b, a)
assert distance == 6
def test_rooted_rf_same_tree():
a = make_tree(treestring="((a, b), (c, d));")
b = make_tree(treestring="((c, d), (a, b));")
# The distance between trees of the same topology is 0
distance = rooted_robinson_foulds(a, b)
assert distance == 0
# matching cluster distance
def test_matching_cluster_distance_multifurcation():
# The basic example from the matching cluster distance paper
# see reference in matching_cluster_distance
a = make_tree(treestring="((a, b), (c, d));")
b = make_tree(treestring="((a, c, b), d);")
distance = matching_cluster_distance(a, b)
assert distance == 3
distance = matching_cluster_distance(b, a)
assert distance == 3
def test_matching_cluster_distance_properties():
# Test properties of the matching cluster distance paper shown as exampels
# see reference in matching_cluster_distance
a = make_tree(
treestring="((((a1,a2),(b1,b2,b3),x),(c1,c2,c3),(d1,d2)),(e1,(e2,e3)));"
)
b = make_tree(
treestring="((((a1,a2),(b1,b2,b3)),x,(c1,c2,c3),(d1,d2)),(e1,(e2,e3)));"
)
distance = matching_cluster_distance(a, b)
assert distance == 1
distance = matching_cluster_distance(b, a)
assert distance == 1
a = make_tree(treestring="((a,b),c);")
b = make_tree(treestring="((a,c),b);")
distance = matching_cluster_distance(a, b)
assert distance == len(a.tips()) - 1
distance = matching_cluster_distance(b, a)
assert distance == len(a.tips()) - 1
a = make_tree(treestring="((a,(b1,(b2,b3))),((c1,c2),(c3,c4)));")
b = make_tree(treestring="((a,((c1,c2),(c3,c4))),(b1,(b2,b3)));")
distance = matching_cluster_distance(a, b)
assert distance == len(a.tips()) - 1
distance = matching_cluster_distance(b, a)
assert distance == len(a.tips()) - 1
def test_matching_cluster_distance_same_tree():
a = make_tree(treestring="((a, b), (c, d));")
b = make_tree(treestring="((c, d), (a, b));")
# The distance between trees of the same topology is 0
distance = matching_cluster_distance(a, b)
assert distance == 0
# different tips
@pytest.mark.parametrize(
"b",
(
"(e, d, (a, b));",
"(a, d, (a, b));",
"(a, b, (c, (d, e)));",
),
)
def test_unrooted_rf_fails_different_tips(b):
t1 = make_tree(treestring="(a, b, (c, d));")
t2 = make_tree(treestring=b)
with pytest.raises(ValueError):
unrooted_robinson_foulds(t1, t2)
with pytest.raises(ValueError):
unrooted_robinson_foulds(t2, t1)
@pytest.mark.parametrize(
"b",
(
"(e, d, (a, b));",
"(a, d, (a, b));",
"(a, b, (c, (d, e)));",
),
)
def test_lrm_fails_different_tips(b):
t1 = make_tree(treestring="(a, b, (c, d));")
t2 = make_tree(treestring=b)
with pytest.raises(ValueError):
lin_rajan_moret(t1, t2)
with pytest.raises(ValueError):
lin_rajan_moret(t2, t1)
@pytest.mark.parametrize(
"b",
(
"((e, d), (a, b));",
"((a, d), (a, b));",
"(a, (b, (c, (d, e))));",
),
)
def test_rooted_rf_fails_different_tips(b):
t1 = make_tree(treestring="((a, b), (c, d));")
t2 = make_tree(treestring=b)
with pytest.raises(ValueError):
rooted_robinson_foulds(t1, t2)
with pytest.raises(ValueError):
rooted_robinson_foulds(t2, t1)
@pytest.mark.parametrize(
"b",
(
"((e, d), (a, b));",
"((a, d), (a, b));",
"(a, (b, (c, (d, e))));",
),
)
def test_matching_cluster_fails_different_tips(b):
t1 = make_tree(treestring="((a, b), (c, d));")
t2 = make_tree(treestring=b)
with pytest.raises(ValueError):
matching_cluster_distance(t1, t2)
with pytest.raises(ValueError):
matching_cluster_distance(t2, t1)
# unrooted distance measures applied to examples with rooted trees
@pytest.mark.parametrize(
"a,b",
(
("((a, b), (c, d));", "(d, c, (a, b));"),
("(a, b, (c, d));", "((d, c), (a, b));"),
("((a, b), (c, d));", "((a, c), (b, d));"),
),
)
def test_unrooted_dist_fails_rooted_trees(a, b):
t1 = make_tree(treestring=a)
t2 = make_tree(treestring=b)
for unrooted_distance_measure in UNROOTED_DISTANCE_MEASURES:
with pytest.raises(ValueError):
unrooted_distance_measure(t1, t2)
# rooted distance measures applied to examples with unrooted trees
@pytest.mark.parametrize(
"a,b",
(
("((a, b), (c, d));", "(d, c, (a, b));"),
("(a, b, (c, d));", "((d, c), (a, b));"),
("(a, b, (c, d));", "(d, c, (a, b));"),
),
)
def test_rooted_dist_fails_unrooted_trees(a, b):
t1 = make_tree(treestring=a)
t2 = make_tree(treestring=b)
for rooted_distance_measure in ROOTED_DISTANCE_MEASURES:
with pytest.raises(ValueError):
rooted_distance_measure(t1, t2)
|
