def test_natsel_timehet(self):
"""natsel_timehet works"""
opt = dict(max_evaluations=2, limit_action="ignore")
aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
natsel = evo_app.natsel_timehet(
"MG94HKY",
tree="data/primate_brca1.tree",
tip1="Human",
tip2="Chimpanzee",
opt_args=opt,
)
result = natsel(aln)
self.assertEqual(result.df, 1)
# the naming scheme is model name followed by null/alt
self.assertTrue("MG94HKY-null" in result)
self.assertTrue("MG94HKY-alt" in result)
# that is_independent works
natsel = evo_app.natsel_timehet(
"MG94HKY",
tree="data/primate_brca1.tree",
tip1="Human",
tip2="Chimpanzee",
is_independent=True,
opt_args=opt,
)
result = natsel(aln)
self.assertEqual(result.df, 2)
# handle specifying just single edge
natsel = evo_app.natsel_timehet("MG94HKY",
tree="data/primate_brca1.tree",
tip1="Human",
opt_args=opt)
result = natsel(aln)
self.assertEqual(result.df, 1)
# fails if not a codon model
with self.assertRaises(ValueError):
_ = evo_app.natsel_timehet("F81", tip1="Human")
def test_natsel_timehet_mprobs(self):
"""natsel_timehet works with gc and mprobs settings"""
opt = dict(max_evaluations=2, limit_action="ignore")
aln = load_aligned_seqs("data/ENSG00000198712.fa", moltype="dna")
natsel = evo_app.natsel_timehet(
"MG94HKY",
tip1="Human",
tip2="Chimp",
opt_args=opt,
gc=2,
optimise_motif_probs=True,
)
result = natsel(aln)
self.assertEqual(result.df, 1)
self.assertEqual(result.null.lf.nfp, 3 + 3 + 1 + 1)
self.assertEqual(result.alt.lf.nfp, 3 + 3 + 1 + 2)
# the naming scheme is model name followed by null/alt
self.assertTrue("MG94HKY-null" in result)
self.assertTrue("MG94HKY-alt" in result)
