def adaptPredicate(self, pred, label=None):
if isinstance(pred, str):
pred = predicate.parse(pred)
elif callable(pred):
pred = predicate.UserPredicate(pred)
pred_func = pred.makeModelPredicate(self)
label = label or repr(pred)
mask = predicate2matrix(
self.getAlphabet(), pred_func, mask=self._instantaneous_mask)
return (label, mask)
def adaptPredicate(self, pred, label=None):
if isinstance(pred, str):
pred = predicate.parse(pred)
elif callable(pred):
pred = predicate.UserPredicate(pred)
pred_func = pred.makeModelPredicate(self)
label = label or repr(pred)
mask = predicate2matrix(
self.getAlphabet(), pred_func, mask=self._instantaneous_mask)
return (label, mask)
def getPredefinedPredicates(self):
gc = self.getAlphabet().getGeneticCode()
def silent(x, y):
return x != '---' and y != '---' and gc[x] == gc[y]
def replacement(x, y):
return x != '---' and y != '---' and gc[x] != gc[y]
preds = _Nucleotide.getPredefinedPredicates(self)
preds.update({
'indel' : predicate.parse('???/---'),
'silent' : predicate.UserPredicate(silent),
'replacement' : predicate.UserPredicate(replacement),
})
return preds
def getPredefinedPredicates(self):
gc = self.getAlphabet().getGeneticCode()
def silent(x, y):
return x != '---' and y != '---' and gc[x] == gc[y]
def replacement(x, y):
return x != '---' and y != '---' and gc[x] != gc[y]
preds = _Nucleotide.getPredefinedPredicates(self)
preds.update({
'indel' : predicate.parse('???/---'),
'silent' : predicate.UserPredicate(silent),
'replacement' : predicate.UserPredicate(replacement),
})
return preds
def getPredefinedPredicates(self):
return {
'transition' : predicate.parse('R/R') | predicate.parse('Y/Y'),
'transversion' : predicate.parse('R/Y'),
'indel': predicate.parse('-/?'),
}
def getPredefinedPredicates(self):
# overridden in subclasses
return {'indel': predicate.parse('-/?')}
def getPredefinedPredicates(self):
return {
'transition': predicate.parse('R/R') | predicate.parse('Y/Y'),
'transversion': predicate.parse('R/Y'),
'indel': predicate.parse('-/?'),
}
def getPredefinedPredicates(self):
# overridden in subclasses
return {'indel': predicate.parse('-/?')}
if self.alphabet[-1] == '---':
Q[:-1, :-1] *= mprobs_matrix[:-1, :-1]
pi = numpy.array(word_probs)
pi /= pi.sum()
Q[-1, :-1] *= pi[:-1]
Q[:-1, -1] *= pi[-1]
else:
Q *= mprobs_matrix
row_totals = Q.sum(axis=1)
Q -= numpy.diag(row_totals)
if self._do_scaling:
Q *= 1.0 / (word_probs * row_totals).sum()
return Q
_gap_preds = [parse('--->???'), parse('???>---')]
_indel = ModelSays('indel')
class MonkeyPatchModel(object):
def makeLikelihoodFunction(self,
tree,
motif_probs_from_align=None,
optimise_motif_probs=None,
aligned=True,
expm=None,
digits=None,
space=None,
**kw):
if motif_probs_from_align is None:
motif_probs_from_align = self.motif_probs_from_align