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|
import os
import pathlib
import unittest
import warnings
from tempfile import TemporaryDirectory
from numpy import exp, log
from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
from cogent3.phylo.consensus import get_splits, get_tree, majority_rule
from cogent3.phylo.least_squares import wls
from cogent3.phylo.maximum_likelihood import ML
from cogent3.phylo.nj import gnj, nj
from cogent3.phylo.tree_collection import (
LogLikelihoodScoredTreeCollection,
ScoredTreeCollection,
WeightedTreeCollection,
make_trees,
)
from cogent3.util.io import remove_files
warnings.filterwarnings("ignore", "Not using MPI as mpi4py not found")
base_path = os.path.dirname(__file__)
data_path = os.path.join(base_path, "data")
def Tree(t):
return make_tree(treestring=t)
class ConsensusTests(unittest.TestCase):
def setUp(self):
self.trees = [
Tree("((a,b),c,d);"),
Tree("((a,b),c,d);"),
Tree("((a,c),b,d);"),
Tree("((a,b),c,d);"),
]
# emphasizing the a,b clade
weights = list(map(log, [0.4, 0.4, 0.05, 0.15]))
self.scored_trees = list(zip(weights, self.trees))
self.scored_trees.sort(reverse=True)
self.rooted_trees = [
Tree("((a,b),(c,d));"),
Tree("((a,b),(c,d));"),
Tree("((a,c),(b,d));"),
Tree("((a,b),c,d);"),
]
self.trees_randomly_rooted = [
(
-3416.3820971172017,
Tree(
"(((F,(M,(P,(K,J)))),A),Q,(H,((S,(X,((Z,N),((O,(L,D)),E)))),((G,((I,(R,T)),Y)),(C,(((U,W),V),B))))));"
),
),
(
-3416.3820974814785,
Tree(
"(R,T,(I,(Y,(G,((((X,((Z,N),((O,(L,D)),E))),S),((Q,((F,(M,(P,(K,J)))),A)),H)),((((U,W),V),C),B))))));"
),
),
(
-3416.571172739171,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(S,((X,((Z,N),((O,(L,D)),E))),(((G,((I,(R,T)),Y)),C),(((U,W),V),B)))))));"
),
),
(
-3416.5721393589474,
Tree(
"(P,(K,J),(M,(F,(A,(Q,(H,(((((Z,N),((O,(L,D)),E)),S),X),((C,(G,((I,(R,T)),Y))),(((U,W),V),B)))))))));"
),
),
(
-3416.5721493054643,
Tree(
"(R,T,(I,(Y,(G,(C,((S,(X,((Z,N),((O,(L,D)),E)))),((((U,W),V),B),((Q,((F,(M,(P,(K,J)))),A)),H))))))));"
),
),
(
-3416.572149424391,
Tree(
"((U,W),V,(B,(((G,((I,(R,T)),Y)),C),((S,(X,((Z,N),((O,(L,D)),E)))),(H,(Q,((F,(M,(P,(K,J)))),A)))))));"
),
),
(
-3416.596424489769,
Tree(
"(S,(X,((Z,N),((O,(L,D)),E))),((((G,((I,(R,T)),Y)),C),(((U,W),V),B)),((H,Q),((F,(M,(P,(K,J)))),A))));"
),
),
(
-3416.6335053806333,
Tree(
"(M,(P,(K,J)),(F,(A,(Q,(H,(((((((O,(L,D)),E),N),Z),X),S),((C,((V,(U,W)),B)),(G,((I,(R,T)),Y)))))))));"
),
),
(
-3416.7626687401867,
Tree(
"(Z,N,(((O,(L,D)),E),(X,(S,((((F,(M,(P,(K,J)))),A),Q),(H,((G,((I,(R,T)),Y)),(C,(((U,W),V),B)))))))));"
),
),
(
-3416.7670692165866,
Tree(
"(X,((Z,N),((O,(L,D)),E)),(S,((B,(((G,((I,(R,T)),Y)),C),((U,W),V))),((Q,((F,(M,(P,(K,J)))),A)),H))));"
),
),
(
-3416.7670696377254,
Tree(
"(P,(K,J),(M,(F,(A,(Q,(H,(((X,((Z,N),((O,(L,D)),E))),S),(((U,W),V),(((G,((I,(R,T)),Y)),C),B)))))))));"
),
),
(
-3416.848062302587,
Tree(
"(((O,(L,D)),E),N,(Z,(X,(S,(((((F,(M,(P,(K,J)))),A),Q),H),(((V,(U,W)),B),(C,(G,((I,(R,T)),Y)))))))));"
),
),
(
-3416.9943503002764,
Tree(
"((U,W),V,(B,((C,(G,((I,(R,T)),Y))),(H,(((((Z,N),((O,(L,D)),E)),S),X),(((F,(M,(P,(K,J)))),A),Q))))));"
),
),
(
-3417.014782481302,
Tree(
"(Q,((F,(M,(P,(K,J)))),A),(((((U,W),V),B),((G,((I,(R,T)),Y)),C)),((S,(X,((Z,N),((O,(L,D)),E)))),H)));"
),
),
(
-3417.015470262783,
Tree(
"(L,D,(O,(E,((Z,N),(X,(S,((Q,((F,(M,(P,(K,J)))),A)),(H,((((U,W),V),B),((G,((I,(R,T)),Y)),C))))))))));"
),
),
(
-3417.241619414339,
Tree(
"(Z,N,(((O,(L,D)),E),(X,(S,(H,((Q,((F,(M,(P,(K,J)))),A)),(B,(((G,((I,(R,T)),Y)),C),((U,W),V)))))))));"
),
),
(
-3417.242009280534,
Tree(
"(X,((Z,N),((O,(L,D)),E)),(S,((Q,((F,(M,(P,(K,J)))),A)),(H,(B,(((G,((I,(R,T)),Y)),C),((U,W),V)))))));"
),
),
(
-3417.2637092520818,
Tree(
"(K,J,(P,(M,(F,(A,(Q,(((((((O,(L,D)),E),N),Z),X),S),(((B,(V,(U,W))),(C,(G,((I,(R,T)),Y)))),H))))))));"
),
),
(
-3417.420526572887,
Tree(
"(B,(V,(U,W)),(((H,(Q,(A,(F,(M,(P,(K,J))))))),((((((O,(L,D)),E),N),X),Z),S)),(C,(((I,(R,T)),Y),G))));"
),
),
(
-3417.4205266767162,
Tree(
"(R,T,(I,(Y,(G,(C,((B,(V,(U,W))),((H,((A,(F,(M,(P,(K,J))))),Q)),(Z,(((((O,(L,D)),E),N),X),S)))))))));"
),
),
(
-3417.620921910812,
Tree(
"((O,(L,D)),E,(N,(X,(Z,(S,(((Q,(A,(F,(M,(P,(K,J)))))),H),((((((I,(R,T)),Y),G),C),(V,(U,W))),B)))))));"
),
),
(
-3417.6209219461302,
Tree(
"(F,(M,(P,(K,J))),(A,(Q,(H,((Z,(((((O,(L,D)),E),N),X),S)),((((G,((I,(R,T)),Y)),C),(V,(U,W))),B))))));"
),
),
(
-3417.6209224304744,
Tree(
"(H,((A,(F,(M,(P,(K,J))))),Q),(B,((Z,(((((O,(L,D)),E),N),X),S)),(((G,((I,(R,T)),Y)),C),(V,(U,W))))));"
),
),
(
-3417.9379715010136,
Tree(
"((I,(R,T)),Y,(G,(C,((B,(V,(U,W))),(H,((Q,(A,(F,(M,(P,(K,J)))))),((((((O,(L,D)),E),N),X),Z),S)))))));"
),
),
(
-3417.9379715187215,
Tree(
"(((O,(L,D)),E),N,(X,(S,(Z,(((A,(F,(M,(P,(K,J))))),Q),(((B,(V,(U,W))),(C,(G,((I,(R,T)),Y)))),H))))));"
),
),
]
self.trees_rooted_at_A = [
(
-3416.3820971172017,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,((S,(X,((Z,N),((O,(L,D)),E)))),((G,((I,(R,T)),Y)),(C,(((U,W),V),B)))))));"
),
),
(
-3416.3820974814785,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(((X,((Z,N),((O,(L,D)),E))),S),((G,((I,(R,T)),Y)),((((U,W),V),C),B))))));"
),
),
(
-3416.571172739171,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(S,((X,((Z,N),((O,(L,D)),E))),(((G,((I,(R,T)),Y)),C),(((U,W),V),B)))))));"
),
),
(
-3416.5721393589474,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(((((Z,N),((O,(L,D)),E)),S),X),((C,(G,((I,(R,T)),Y))),(((U,W),V),B))))));"
),
),
(
-3416.5721493054643,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,((((U,W),V),B),(((G,((I,(R,T)),Y)),C),(S,(X,((Z,N),((O,(L,D)),E)))))))));"
),
),
(
-3416.572149424391,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,((S,(X,((Z,N),((O,(L,D)),E)))),(((G,((I,(R,T)),Y)),C),(((U,W),V),B))))));"
),
),
(
-3416.596424489769,
Tree(
"((F,(M,(P,(K,J)))),A,(((S,(X,((Z,N),((O,(L,D)),E)))),(((G,((I,(R,T)),Y)),C),(((U,W),V),B))),(H,Q)));"
),
),
(
-3416.6335053806333,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(((((((O,(L,D)),E),N),Z),X),S),((C,((V,(U,W)),B)),(G,((I,(R,T)),Y)))))));"
),
),
(
-3416.7626687401867,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,((H,((G,((I,(R,T)),Y)),(C,(((U,W),V),B)))),(S,(X,((Z,N),((O,(L,D)),E)))))));"
),
),
(
-3416.7670692165866,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(((B,(((G,((I,(R,T)),Y)),C),((U,W),V))),((X,((Z,N),((O,(L,D)),E))),S)),H)));"
),
),
(
-3416.7670696377254,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(((X,((Z,N),((O,(L,D)),E))),S),(((U,W),V),(((G,((I,(R,T)),Y)),C),B))))));"
),
),
(
-3416.848062302587,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(H,(((((((O,(L,D)),E),N),Z),X),S),(((V,(U,W)),B),(C,(G,((I,(R,T)),Y))))))));"
),
),
(
-3416.9943503002764,
Tree(
"((F,(M,(P,(K,J)))),A,(((((C,(G,((I,(R,T)),Y))),(((U,W),V),B)),H),((((Z,N),((O,(L,D)),E)),S),X)),Q));"
),
),
(
-3417.014782481302,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(((((U,W),V),B),((G,((I,(R,T)),Y)),C)),((S,(X,((Z,N),((O,(L,D)),E)))),H))));"
),
),
(
-3417.015470262783,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,((H,((((U,W),V),B),((G,((I,(R,T)),Y)),C))),(S,(X,((Z,N),((O,(L,D)),E)))))));"
),
),
(
-3417.241619414339,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,((H,((X,((Z,N),((O,(L,D)),E))),S)),(B,(((G,((I,(R,T)),Y)),C),((U,W),V))))));"
),
),
(
-3417.242009280534,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(((X,((Z,N),((O,(L,D)),E))),S),(H,(B,(((G,((I,(R,T)),Y)),C),((U,W),V)))))));"
),
),
(
-3417.2637092520818,
Tree(
"((F,(M,(P,(K,J)))),A,(Q,(((((((O,(L,D)),E),N),Z),X),S),(((B,(V,(U,W))),(C,(G,((I,(R,T)),Y)))),H))));"
),
),
(
-3417.420526572887,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,(H,(((((((O,(L,D)),E),N),X),Z),S),((B,(V,(U,W))),(C,(((I,(R,T)),Y),G)))))));"
),
),
(
-3417.4205266767162,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,(H,(((B,(V,(U,W))),(C,(G,((I,(R,T)),Y)))),(Z,(((((O,(L,D)),E),N),X),S))))));"
),
),
(
-3417.620921910812,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,(H,(((((((O,(L,D)),E),N),X),Z),S),((((((I,(R,T)),Y),G),C),(V,(U,W))),B)))));"
),
),
(
-3417.6209219461302,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,(H,((Z,(((((O,(L,D)),E),N),X),S)),((((G,((I,(R,T)),Y)),C),(V,(U,W))),B)))));"
),
),
(
-3417.6209224304744,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,(H,(B,((Z,(((((O,(L,D)),E),N),X),S)),(((G,((I,(R,T)),Y)),C),(V,(U,W))))))));"
),
),
(
-3417.9379715010136,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,((H,((B,(V,(U,W))),(C,(((I,(R,T)),Y),G)))),((((((O,(L,D)),E),N),X),Z),S))));"
),
),
(
-3417.9379715187215,
Tree(
"(A,(F,(M,(P,(K,J)))),(Q,((Z,(((((O,(L,D)),E),N),X),S)),(((B,(V,(U,W))),(C,(G,((I,(R,T)),Y)))),H))));"
),
),
]
self.unrooted_conflicting_trees = [
Tree("((a,b),c,d);"),
Tree("((a,c),b,d);"),
Tree("((a,d),b,c);"),
]
self.rooted_conflicting_trees = [
Tree("((a,b),(c,d));"),
Tree("((a,c),(b,d));"),
Tree("((a,d),(b,c));"),
]
self.unrooted_trees_lengths = [
(2, Tree("((a:0.3,c:0.4):0.5,b:0.2,d:0.1);")),
(1, Tree("((a:0.1,b:0.1):0.1,c:0.1,d:0.1);")),
]
self.rooted_trees_lengths = [
(2, Tree("((a:0.3,c:0.4):0.2,(b:0.2,d:0.1):0.3);")),
(1, Tree("((a:0.1,b:0.1):0.05,(c:0.1,d:0.1):0.05);")),
]
def test_majorityRule(self):
"""Tests for majority rule consensus trees"""
trees = self.rooted_trees
outtrees = majority_rule(trees, strict=False)
self.assertEqual(len(outtrees), 1)
self.assertTrue(outtrees[0].same_topology(Tree("((c,d),(a,b));")))
outtrees = majority_rule(trees, strict=True)
self.assertEqual(len(outtrees), 1)
self.assertTrue(outtrees[0].same_topology(Tree("(c,d,(a,b));")))
def test_get_tree_get_splits(self):
"""get_tree should provide a reciprocal map of get_splits"""
tree = load_tree(os.path.join(data_path, "murphy.tree"))
self.assertTrue(tree.same_topology(get_tree(get_splits(tree))))
def test_consensus_tree_branch_lengths(self):
"""consensus trees should average branch lengths properly"""
def get_ac(tree):
for edge in tree.get_edge_vector(include_root=False):
if set("ac") == set([c.name for c in edge.children]):
return edge
sct = ScoredTreeCollection(self.unrooted_trees_lengths)
ct = sct.get_consensus_tree()
maj_tree = self.unrooted_trees_lengths[0][1]
# to ensure consistent comparison with majority, we root the ct same way
# as maj
tip_names = maj_tree.get_tip_names()
ct = ct.rooted_with_tip("d")
ct = ct.sorted(tip_names)
self.assertTrue(abs(get_ac(ct).length - get_ac(maj_tree).length) < 1e-9)
sct = ScoredTreeCollection(self.rooted_trees_lengths)
ct = sct.get_consensus_tree(method="rooted")
maj_tree = self.rooted_trees_lengths[0][1]
self.assertTrue(abs(get_ac(ct).length - get_ac(maj_tree).length) < 1e-9)
def test_scored_trees_collection_write(self):
"""writes a tree collection"""
sct = ScoredTreeCollection(self.rooted_trees_lengths)
with TemporaryDirectory(".") as dirname:
dirname = pathlib.Path(dirname)
out = dirname / "collection.trees"
sct.write(out)
def test_consensus_from_scored_trees_collection(self):
"""tree collection should get same consensus as direct approach"""
tree_list = [(i * -1, t) for i, t in enumerate(self.trees)]
sct = LogLikelihoodScoredTreeCollection(tree_list)
ct = sct.get_consensus_tree()
self.assertTrue(ct.same_topology(Tree("((c,d),a,b);")))
def test_consensus_from_scored_trees_collection_ii(self):
"""strict consensus should handle conflicting trees"""
sct = ScoredTreeCollection(list(zip([1] * 3, self.unrooted_conflicting_trees)))
ct = sct.get_consensus_trees()[0]
self.assertTrue(ct.same_topology(Tree("(a,b,c,d);")))
sct = ScoredTreeCollection(list(zip([1] * 3, self.rooted_conflicting_trees)))
# cts = sct.get_consensus_trees(method='rooted')
ct = sct.get_consensus_trees(method="rooted")[0]
self.assertTrue(ct.same_topology(Tree("(a,b,c,d);")))
# for tree in cts:
# print str(tree)
# self.assertTrue(set(map(str, cts))==set(['('+c+');' for c in 'abcd']))
def test_weighted_consensus_from_scored_trees_collection(self):
"""weighted consensus from a tree collection should be different"""
sct = LogLikelihoodScoredTreeCollection(self.scored_trees)
ct = sct.get_consensus_tree()
self.assertTrue(ct.same_topology(Tree("((a,b),c,d);")))
def test_weighted_consensus_from_scored_trees_collection_ii(self):
"""root positions in input tree collection should not effect result"""
sct = LogLikelihoodScoredTreeCollection(self.trees_randomly_rooted)
ctrr = sct.get_consensus_tree()
sct = LogLikelihoodScoredTreeCollection(self.trees_rooted_at_A)
ctra = sct.get_consensus_tree()
self.assertTrue(ctrr.same_topology(ctra))
def test_weighted_trees_satisyfing_cutoff(self):
"""build consensus tree from those satisfying cutoff"""
sct = LogLikelihoodScoredTreeCollection(self.scored_trees)
cts = sct.get_weighted_trees(cutoff=0.8)
for weight, tree in cts:
self.assertTrue(tree.same_topology(Tree("((a,b),c,d);")))
ct = cts.get_consensus_tree()
self.assertTrue(ct.same_topology(Tree("((a,b),c,d);")))
def test_tree_collection_read_write_file(self):
"""should correctly read / write a collection from a file"""
def eval_klass(coll):
coll.write("sample.trees")
read = make_trees("sample.trees")
self.assertTrue(type(read) == type(coll))
eval_klass(LogLikelihoodScoredTreeCollection(self.scored_trees))
# convert lnL into p
eval_klass(WeightedTreeCollection([(exp(s), t) for s, t in self.scored_trees]))
remove_files(["sample.trees"], error_on_missing=False)
class TreeReconstructionTests(unittest.TestCase):
def setUp(self):
self.tree = make_tree(treestring="((a:3,b:4):2,(c:6,d:7):30,(e:5,f:5):5)")
self.dists = self.tree.get_distances()
def assertTreeDistancesEqual(self, t1, t2):
d1 = t1.get_distances()
d2 = t2.get_distances()
self.assertEqual(len(d1), len(d2))
for key in d2:
self.assertAlmostEqual(d1[key], d2[key])
def test_nj(self):
"""testing nj"""
reconstructed = nj(self.dists, show_progress=False)
self.assertTreeDistancesEqual(self.tree, reconstructed)
def test_gnj(self):
"""testing gnj"""
results = gnj(self.dists, keep=1, show_progress=False)
(length, reconstructed) = results[0]
self.assertTreeDistancesEqual(self.tree, reconstructed)
results = gnj(self.dists, keep=10, show_progress=False)
(length, reconstructed) = results[0]
self.assertTreeDistancesEqual(self.tree, reconstructed)
# Results should be a TreeCollection
results.get_consensus_tree()
# From GNJ paper. Pearson, Robins, Zhang 1999.
tied_dists = {
("a", "b"): 3,
("a", "c"): 3,
("a", "d"): 4,
("a", "e"): 3,
("b", "c"): 3,
("b", "d"): 3,
("b", "e"): 4,
("c", "d"): 3,
("c", "e"): 3,
("d", "e"): 3,
}
results = gnj(tied_dists, keep=3, show_progress=False)
scores = [score for (score, tree) in results]
self.assertEqual(scores[:2], [7.75, 7.75])
self.assertNotEqual(scores[2], 7.75)
def test_wls(self):
"""testing wls"""
reconstructed = wls(self.dists, a=4, show_progress=False)
self.assertTreeDistancesEqual(self.tree, reconstructed)
def test_truncated_wls(self):
"""testing wls with order option"""
order = ["e", "b", "c", "d"]
reconstructed = wls(self.dists, order=order, show_progress=False)
self.assertEqual(set(reconstructed.get_tip_names()), set(order))
def test_limited_wls(self):
"""testing (well, exercising at least), wls with constrained start"""
init = make_tree(treestring="((a,c),b,d)")
reconstructed = wls(self.dists, start=init, show_progress=False)
self.assertEqual(len(reconstructed.get_tip_names()), 6)
init2 = make_tree(treestring="((a,d),b,c)")
reconstructed = wls(self.dists, start=[init, init2], show_progress=False)
self.assertEqual(len(reconstructed.get_tip_names()), 6)
init3 = make_tree(treestring="((a,d),b,z)")
self.assertRaises(Exception, wls, self.dists, start=[init, init3])
# if start tree has all seq names, should raise an error
self.assertRaises(
Exception,
wls,
self.dists,
start=[make_tree(treestring="((a,c),b,(d,(e,f)))")],
)
def test_ml(self):
"""exercise the ML tree estimation"""
from numpy.testing import assert_allclose
aln = load_aligned_seqs(os.path.join(data_path, "brca1.fasta"), moltype="dna")
aln = aln.take_seqs(["Human", "Mouse", "Rat", "Dog"])
aln = aln.omit_gap_pos(allowed_gap_frac=0)
model = get_model("JC69")
lnL, tree = ML(model, aln).trex(a=3, k=1, show_progress=False)
assert_allclose(lnL, -8882.217502905267)
self.assertTrue(tree.same_topology(make_tree("(Mouse,Rat,(Human,Dog));")))
def test_gnj_two():
"""testing gnj when just 2 taxa"""
dists = {("a", "b"): 1, ("b", "a"): 1}
results = gnj(dists, keep=1, show_progress=False)
length, got = results[0]
assert set(got.get_tip_names()) == {"a", "b"}
assert length == 1.0
assert got.name == "root"
assert len(got.children) == 2
assert {e.length for e in got.postorder(include_self=False)} == {0.5}
def test_nj_two():
"""testing gnj when just 2 taxa"""
dists = {("a", "b"): 1, ("b", "a"): 1}
got = nj(dists, show_progress=False)
assert set(got.get_tip_names()) == {"a", "b"}
assert got.name == "root"
assert len(got.children) == 2
assert {e.length for e in got.postorder(include_self=False)} == {0.5}
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