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_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)