예제 #1
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 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)
예제 #2
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 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)
예제 #3
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 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()
예제 #4
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 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()