def test_parse(self):
"""correctly construction"""
ag = MotifChange("A", "G")
got = parse(str(ag))
self.assertEqual(str(got), "A/G")
ts = MotifChange("A", "G") | MotifChange("C", "T")
got = parse(str(ts))
self.assertEqual(str(got), "(A/G | C/T)")
a_g = MotifChange("A", "G", forward_only=True)
t_c = MotifChange("T", "C", forward_only=True)
sym = a_g | t_c
got = parse(str(sym))
self.assertEqual(str(got), "(A>G | T>C)")
def adapt_predicate(self, pred, label=None):
if isinstance(pred, str):
pred = predicate.parse(pred)
elif isinstance(pred, Callable):
pred = predicate.UserPredicate(pred)
pred_func = pred.make_model_predicate(self)
label = label or repr(pred)
mask = predicate2matrix(self.get_alphabet(),
pred_func,
mask=self._instantaneous_mask)
return (label, mask)
def get_predefined_predicates(self):
return {
"transition": predicate.parse("R/R") | predicate.parse("Y/Y"),
"transversion": predicate.parse("R/Y"),
"indel": predicate.parse("-/?"),
"kappa": (predicate.parse("R/R") | predicate.parse("Y/Y")).aliased("kappa"),
}
def get_predefined_predicates(self):
codon_preds = _CodonPredicates(self.get_alphabet().get_genetic_code())
preds = _TimeReversibleNucleotide.get_predefined_predicates(self)
preds.update(
{
"indel": predicate.parse("???/---"),
"silent": predicate.UserPredicate(codon_preds.silent),
"replacement": predicate.UserPredicate(codon_preds.replacement),
"omega": predicate.UserPredicate(codon_preds.replacement),
}
)
return preds
def get_predefined_predicates(self):
# overridden in subclasses
return {"indel": predicate.parse("-/?")}
