def _get_all_composables(tmp_dir_name):
test_model1 = evo.model("HKY85")
test_model2 = evo.model("GN")
test_hyp = evo.hypothesis(test_model1, test_model2)
test_num_reps = 100
applications = [
align.align_to_ref(),
align.progressive_align(model="GY94"),
evo.ancestral_states(),
evo.bootstrap(hyp=test_hyp, num_reps=test_num_reps),
evo.hypothesis(test_model1, test_model2),
evo.model("GN"),
evo.tabulate_stats(),
sample.fixed_length(100),
sample.min_length(100),
io.write_db(tmp_dir_name, create=True),
io.write_json(tmp_dir_name, create=True),
io.write_seqs(tmp_dir_name, create=True),
sample.omit_bad_seqs(),
sample.omit_degenerates(),
sample.omit_duplicated(),
sample.take_codon_positions(1),
sample.take_named_seqs(),
sample.trim_stop_codons(gc=1),
translate.select_translatable(),
tree.quick_tree(),
tree.scale_branches(),
tree.uniformize_tree(),
]
return applications
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)
