def test_gnj(self):
"""testing gnj"""
results = gnj(self.dists, keep=1)
(length, reconstructed) = results[0]
self.assertTreeDistancesEqual(self.tree, reconstructed)
results = gnj(self.dists, keep=10)
(length, reconstructed) = results[0]
self.assertTreeDistancesEqual(self.tree, reconstructed)
# Results should be a TreeCollection
len(results)
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)
scores = [score for (score, tree) in results]
self.assertEqual(scores[:2], [7.75, 7.75])
self.assertNotEqual(scores[2], 7.75)
def quick_tree(self, dists):
"""estimates a neighbor joining tree"""
size = dists.shape[0]
dists = dists.drop_invalid() if self._drop_invalid else dists
if dists is None or (dists.shape[0] != size
and not self._drop_invalid):
raise ValueError("invalid pairwise distances")
# how many species do we have
if size == 2:
dist = dists.array[0, 1] / 2.0
newick = ",".join(f"{sp}:{dist:.4f}" for sp in dists.names)
newick = f"({newick})"
tree = make_tree(treestring=newick, underscore_unmunge=True)
else:
(result, ) = gnj(dists.to_dict(), keep=1, show_progress=False)
(score, tree) = result
return tree
def quick_tree(self, dists):
"""estimates a neighbor joining tree"""
size = dists.shape[0]
dists = dists.drop_invalid() if self._drop_invalid else dists
if dists is None or (dists.shape[0] != size
and not self._drop_invalid):
msg = (f"some pairwise distances could not be computed with"
" {self._distance}, pick a different distance")
raise ValueError(msg)
# how many species do we have
species = dists.keys()
if len(species) == 2:
dist = list(dists.values())[0] / 2.0
treestring = "(%s:%.4f,%s:%.4f)" % (species[0], dist, species[1],
dist)
tree = make_tree(treestring=treestring, underscore_unmunge=True)
else:
(result, ) = gnj(dists.to_dict(), keep=1, show_progress=False)
(score, tree) = result
return tree