def test_lf_display(self):
"""str of likelihood functions should not fail"""
for (dummy, model) in self.ordered_by_complexity:
di = Nucleotide(motif_length=2, mprob_model=model)
di.adaptMotifProbs(self.cond_root_probs, auto=True)
lf = di.makeLikelihoodFunction(self.tree)
s = str(lf)
def test_lf_display(self):
"""str of likelihood functions should not fail"""
for (dummy, model) in self.ordered_by_complexity:
di = Nucleotide(motif_length=2, mprob_model=model)
di.adaptMotifProbs(self.cond_root_probs, auto=True)
lf = di.makeLikelihoodFunction(self.tree)
s = str(lf)
def test_reconstruct_ancestor(self):
"""should be able to reconstruct ancestral sequences under all
models"""
for (mprobs, model) in self.ordered_by_complexity:
di = Nucleotide(motif_length=2, mprob_model=model)
di.adaptMotifProbs(mprobs, auto=True)
lf = di.makeLikelihoodFunction(self.tree)
lf.setParamRule('length', is_independent=False, init=0.4)
lf.setAlignment(self.aln)
ancestor = lf.reconstructAncestralSeqs()
def test_reconstruct_ancestor(self):
"""should be able to reconstruct ancestral sequences under all
models"""
for (mprobs, model) in self.ordered_by_complexity:
di = Nucleotide(motif_length=2, mprob_model=model)
di.adaptMotifProbs(mprobs, auto=True)
lf = di.makeLikelihoodFunction(self.tree)
lf.setParamRule('length', is_independent=False, init=0.4)
lf.setAlignment(self.aln)
ancestor = lf.reconstructAncestralSeqs()