def test_neutral_mtdna(self):
"""test of neutrality, different genetic code"""
from cogent3.app.composable import NotCompleted
opt = dict(max_evaluations=2, limit_action="ignore")
aln = load_aligned_seqs("data/ENSG00000198712.fa", moltype="dna")
neutral = evo_app.natsel_neutral("MG94HKY", opt_args=opt, gc=2)
result = neutral(aln)
self.assertEqual(result.df, 1)
# not completed if wrong gc
neutral = evo_app.natsel_neutral("MG94HKY", opt_args=opt, gc=1)
result = neutral(aln)
self.assertIsInstance(result, NotCompleted)
def test_neutral(self):
"""test of neutrality, one omega != 1"""
opt = dict(max_evaluations=20, limit_action="ignore")
aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
neutral = evo_app.natsel_neutral("MG94HKY",
tree="data/primate_brca1.tree",
opt_args=opt)
result = neutral(aln)
self.assertEqual(result.df, 1)
self.assertTrue("MG94HKY-null" in result)
self.assertTrue("MG94HKY-alt" in result)
# fails if not a codon model
with self.assertRaises(ValueError):
_ = evo_app.natsel_neutral("F81", tree="data/primate_brca1.tree")
def test_neutral_mprobs(self):
"""test of neutrality, optimise_motif_probs setting should work"""
opt = dict(max_evaluations=2, limit_action="ignore")
aln = load_aligned_seqs("data/ENSG00000198712.fa", moltype="dna")
# default, not optimising root probs
natsel = evo_app.natsel_neutral("MG94HKY", opt_args=opt, gc=2)
result = natsel(aln)
self.assertEqual(result.null.lf.nfp, 4)
# optimising root probs
natsel = evo_app.natsel_neutral(
"MG94HKY", opt_args=opt, gc=2, optimise_motif_probs=True
)
result = natsel(aln)
self.assertEqual(result.null.lf.nfp, 7)
def test_neutral_nstat_model(self):
"""test of neutrality, non-stationary codon model"""
opt = dict(max_evaluations=2, limit_action="ignore")
aln = load_aligned_seqs("data/ENSG00000198712.fa", moltype="dna")
neutral = evo_app.natsel_neutral("GNC", opt_args=opt, gc=2)
result = neutral(aln)
# 11 rate matrix params for GNC (omega omitted in null), 3 edges
self.assertEqual(result.null.lf.nfp, 3 + 11)
