def test_zhang_mtseq(self):
"""genetic code setting should work"""
from cogent3.app.composable import NotCompleted
opt = dict(max_evaluations=20, limit_action="ignore")
aln = load_aligned_seqs("data/ENSG00000198712.fa", moltype="dna")
natsel = evo_app.natsel_zhang("CNFGTR", tip1="Human", opt_args=opt, gc=2)
result = natsel(aln)
self.assertEqual(result.df, 3)
# but if provide wrong gc, get NotCompleted
natsel = evo_app.natsel_zhang("CNFGTR", tip1="Human", opt_args=opt, gc=1)
result = natsel(aln)
self.assertIsInstance(result, NotCompleted)
def test_zhang_mprobs(self):
"""natsel_zhang 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_zhang("MG94HKY", tip1="Human", opt_args=opt, gc=2)
result = natsel(aln)
self.assertEqual(result.null.lf.nfp, 6)
# optimising root probs
natsel = evo_app.natsel_zhang(
"MG94HKY", tip1="Human", opt_args=opt, gc=2, optimise_motif_probs=True
)
result = natsel(aln)
self.assertEqual(result.null.lf.nfp, 9)
def test_zhang(self):
"""natsel_zhang correctly configured and should not fail"""
opt = dict(max_evaluations=20, limit_action="ignore")
aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
natsel = evo_app.natsel_zhang(
"CNFGTR",
tree="data/primate_brca1.tree",
tip1="Human",
tip2="Chimpanzee",
opt_args=opt,
)
result = natsel(aln)
self.assertEqual(result.df, 3)
self.assertEqual(result.alt.nfp, 21)
# the naming scheme is model name followed by null/alt
self.assertTrue("CNFGTR-null" in result)
self.assertTrue("CNFGTR-alt" in result)
# result keys correct when given a model
Y98 = get_model("Y98")
natsel = evo_app.natsel_zhang(
Y98,
tree="data/primate_brca1.tree",
tip1="Human",
tip2="Chimpanzee",
opt_args=opt,
)
result = natsel(aln)
self.assertEqual(result.df, 3)
self.assertTrue("Y98-null" in result)
self.assertTrue("Y98-alt" in result)
# fails if not a codon model
with self.assertRaises(ValueError):
_ = evo_app.natsel_zhang(
"F81",
tree="data/primate_brca1.tree",
tip1="Human",
tip2="Chimpanzee",
opt_args=opt,
)
# fails if no tip names provided
with self.assertRaises(ValueError):
_ = evo_app.natsel_zhang("Y98",
tree="data/primate_brca1.tree",
opt_args=opt)
