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import os
from unittest import TestCase, main
from cogent3 import DNA, load_aligned_seqs, make_aligned_seqs, make_tree
from cogent3.app import dist
from cogent3.app import tree as tree_app
from cogent3.app.composable import NotCompleted
from cogent3.core.tree import PhyloNode
from cogent3.evolve.fast_distance import DistanceMatrix
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "Alpha"
base_path = os.path.dirname(os.path.dirname(__file__))
data_path = os.path.join(base_path, "data")
class TestTree(TestCase):
def test_scale_tree_lengths(self):
"""correctly scales tree lengths"""
with self.assertRaises(AssertionError):
_ = tree_app.scale_branches(nuc_to_codon=True, codon_to_nuc=True)
scale_to_codon = tree_app.scale_branches(nuc_to_codon=True)
tree = make_tree(treestring="(a:3,b:6,c:9)")
scale_to_codon = tree_app.scale_branches(nuc_to_codon=True)
d = scale_to_codon(tree)
got = {e.name: e.length for e in d.get_edge_vector(include_root=False)}
expect = {"a": 1.0, "b": 2.0, "c": 3.0}
self.assertEqual(got, expect)
scale_from_codon = tree_app.scale_branches(codon_to_nuc=True)
d = scale_from_codon(d)
got = {e.name: e.length for e in d.get_edge_vector(include_root=False)}
expect = {"a": 3.0, "b": 6.0, "c": 9.0}
self.assertEqual(got, expect)
by_scalar = tree_app.scale_branches(scalar=0.5)
d = by_scalar(tree)
got = {e.name: e.length for e in d.get_edge_vector(include_root=False)}
expect = {"a": 6.0, "b": 12.0, "c": 18.0}
self.assertEqual(got, expect)
# handle case where a length is not defined, setting to minimum
min_length = tree_app.scale_branches(min_length=66)
tree = make_tree(treestring="(a:3,b:6,c)")
new = min_length(tree)
got = {e.name: e.length for e in new.get_edge_vector(include_root=False)}
expect = {"a": 3.0, "b": 6.0, "c": 66.0}
self.assertEqual(got, expect)
def test_quick_tree(self):
"""correctly calc a nj tree"""
path = os.path.join(data_path, "brca1_5.paml")
aln = load_aligned_seqs(path, moltype=DNA)
fast_slow_dist = dist.fast_slow_dist(fast_calc="hamming", moltype="dna")
dist_matrix = fast_slow_dist(aln)
quick1 = tree_app.quick_tree()
tree1 = quick1(dist_matrix)
self.assertEqual(set(tree1.get_tip_names()), set(aln.names))
def test_composable_apps(self):
"""checks the ability of these two apps(fast_slow_dist and quick_tree) to communicate"""
path = os.path.join(data_path, "brca1_5.paml")
aln1 = load_aligned_seqs(path, moltype=DNA)
calc_dist = dist.fast_slow_dist(fast_calc="hamming", moltype="dna")
quick = tree_app.quick_tree(drop_invalid=False)
proc = calc_dist + quick
self.assertEqual(
str(proc),
"fast_slow_dist(distance=None, moltype='dna', "
"fast_calc='hamming',\nslow_calc=None) + quick_tree("
"drop_invalid=False)",
)
self.assertIsInstance(proc, tree_app.quick_tree)
self.assertIsInstance(proc.input, dist.fast_slow_dist)
tree1 = proc(aln1)
self.assertIsInstance(tree1, PhyloNode)
self.assertIsNotNone(tree1.children)
self.assertEqual(set(tree1.get_tip_names()), set(aln1.names))
# tests when distances contain None
data = dict(
seq1="AGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT",
)
aln2 = make_aligned_seqs(data=data, moltype=DNA)
tree2 = proc(aln2)
self.assertIsInstance(tree2, NotCompleted)
def test_quick_tree_taking_distance_matrix(self):
"""quick_tree should take a distance matrix"""
quick_tree = tree_app.quick_tree()
data = {
("ABAYE2984", "Avin_42730"): 0.638,
("Atu3667", "Avin_42730"): 2.368,
("Avin_42730", "ABAYE2984"): 0.638,
("Avin_42730", "Atu3667"): 2.368,
("Avin_42730", "BAA10469"): 1.85,
("BAA10469", "Avin_42730"): 1.85,
}
darr = DistanceMatrix(data)
tree = quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(
set(tree.get_tip_names()), set.union(*(set(tup) for tup in data))
)
data = {
("DogFaced", "FlyingFox"): 0.05,
("DogFaced", "FreeTaile"): 0.14,
("DogFaced", "LittleBro"): 0.16,
("DogFaced", "TombBat"): 0.15,
("FlyingFox", "DogFaced"): 0.05,
("FlyingFox", "FreeTaile"): 0.12,
("FlyingFox", "LittleBro"): 0.13,
("FlyingFox", "TombBat"): 0.14,
("FreeTaile", "DogFaced"): 0.14,
("FreeTaile", "FlyingFox"): 0.12,
("FreeTaile", "LittleBro"): 0.09,
("FreeTaile", "TombBat"): 0.1,
("LittleBro", "DogFaced"): 0.16,
("LittleBro", "FlyingFox"): 0.13,
("LittleBro", "FreeTaile"): 0.09,
("LittleBro", "TombBat"): 0.12,
("TombBat", "DogFaced"): 0.15,
("TombBat", "FlyingFox"): 0.14,
("TombBat", "FreeTaile"): 0.1,
("TombBat", "LittleBro"): 0.12,
}
darr = DistanceMatrix(data)
tree = quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(
set(tree.get_tip_names()), set.union(*(set(tup) for tup in data))
)
data = {
("ABAYE2984", "Atu3667"): 0.25,
("ABAYE2984", "Avin_42730"): 0.638,
("ABAYE2984", "BAA10469"): None,
("Atu3667", "ABAYE2984"): 0.25,
("Atu3667", "Avin_42730"): 2.368,
("Atu3667", "BAA10469"): 0.25,
("Avin_42730", "ABAYE2984"): 0.638,
("Avin_42730", "Atu3667"): 2.368,
("Avin_42730", "BAA10469"): 1.85,
("BAA10469", "ABAYE2984"): 0.25,
("BAA10469", "Atu3667"): 0.25,
("BAA10469", "Avin_42730"): 1.85,
}
darr = DistanceMatrix(data)
tree = quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(
set(tree.get_tip_names()), set.union(*(set(tup) for tup in data))
)
data = {
("ABAYE2984", "Atu3667"): None,
("ABAYE2984", "Avin_42730"): 0.638,
("ABAYE2984", "BAA10469"): None,
("Atu3667", "ABAYE2984"): None,
("Atu3667", "Avin_42730"): 2.368,
("Atu3667", "BAA10469"): None,
("Avin_42730", "ABAYE2984"): 0.638,
("Avin_42730", "Atu3667"): 2.368,
("Avin_42730", "BAA10469"): 1.85,
("BAA10469", "ABAYE2984"): None,
("BAA10469", "Atu3667"): None,
("BAA10469", "Avin_42730"): 1.85,
}
darr = DistanceMatrix(data)
# must explicitly call main() method to avoid error trapping by decorator
with self.assertRaises(KeyError):
quick_tree.main(darr)
# when distance_matrix is None after dropping invalid
with self.assertRaises(ValueError):
quick_tree = tree_app.quick_tree(drop_invalid=True)
quick_tree.main(darr)
data = {
("DogFaced", "FlyingFox"): 0.05,
("DogFaced", "FreeTaile"): 0.14,
("DogFaced", "LittleBro"): 0.16,
("DogFaced", "TombBat"): 0.15,
("FlyingFox", "DogFaced"): 0.05,
("FlyingFox", "FreeTaile"): 0.12,
("FlyingFox", "LittleBro"): 0.13,
("FlyingFox", "TombBat"): 0.14,
("FreeTaile", "DogFaced"): 0.14,
("FreeTaile", "FlyingFox"): 0.12,
("FreeTaile", "LittleBro"): 0.09,
("FreeTaile", "TombBat"): 0.1,
("LittleBro", "DogFaced"): 0.16,
("LittleBro", "FlyingFox"): 0.13,
("LittleBro", "FreeTaile"): 0.09,
("LittleBro", "TombBat"): 0.12,
("TombBat", "DogFaced"): 0.15,
("TombBat", "FlyingFox"): 0.14,
("TombBat", "FreeTaile"): 0.1,
("TombBat", "LittleBro"): 0.12,
}
darr = DistanceMatrix(data)
tree = quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(
set(tree.get_tip_names()), set.union(*(set(tup) for tup in data))
)
data = {"a": {"b": 0.1, "a": 0.0}, "b": {"a": 0.1, "b": 0.0}}
darr = DistanceMatrix(data)
tree = quick_tree(darr)
self.assertEqual(
set(tree.get_tip_names()), set.union(*(set(tup) for tup in data))
)
def test_uniformize_tree(self):
"""equivalent topologies should be the same"""
a = make_tree(treestring="(a,(b,c),(d,e))")
b = make_tree(treestring="(e,d,(a,(b,c)))")
make_uniform = tree_app.uniformize_tree(
root_at="c", ordered_names=list("abcde")
)
u_a = make_uniform(a).get_newick()
u_b = make_uniform(b).get_newick()
self.assertTrue(u_a == u_b)
# but different ones different
c = make_tree(treestring="(e,c,(a,(b,d)))")
u_c = make_uniform(c).get_newick()
self.assertFalse(u_a == u_c)
if __name__ == "__main__":
main()
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