def getLocalViterbiScoreAndAlignment(self, posterior_probs=False, **kw):
# Only for pairwise. Merge with getViterbiScoreAndAlignable above.
# Local and POGs doesn't mix well.
(vscore, tb) = self._getDPResult(viterbi=True, local=True, **kw)
(state_directions, T) = self._transition_matrix
aligned_positions = tb.asBinPosTuples(state_directions)
seqs = self.emission_probs.pair.getSeqNamePairs()
aligned_positions = [posn for (bin, posn) in aligned_positions]
word_length = self.emission_probs.pair.alphabet.getMotifLen()
align = alignment_traceback(seqs, aligned_positions, word_length)
if posterior_probs:
pp = self._getPosteriorProbs(tb, use_cost_function=False)
return (vscore, align, numpy.exp(pp))
else:
return (vscore, align)
def getLocalViterbiScoreAndAlignment(self, posterior_probs=False, **kw):
# Only for pairwise. Merge with getViterbiScoreAndAlignable above.
# Local and POGs doesn't mix well.
(vscore, tb) = self._getDPResult(viterbi=True, local=True, **kw)
(state_directions, T) = self._transition_matrix
aligned_positions = tb.asBinPosTuples(state_directions)
seqs = self.emission_probs.pair.getSeqNamePairs()
aligned_positions = [posn for (bin, posn) in aligned_positions]
word_length = self.emission_probs.pair.alphabet.getMotifLen()
align = alignment_traceback(seqs, aligned_positions, word_length)
if posterior_probs:
pp = self._getPosteriorProbs(tb, use_cost_function=False)
return (vscore, align, numpy.exp(pp))
else:
return (vscore, align)
def getAlignment(self):
"""The alignment as a standard PyCogent Alignment object"""
seqs = self.pair_hmm.emission_probs.pair.getSeqNamePairs()
word_length = self.pair_hmm.emission_probs.pair.alphabet.getMotifLen()
aligned_positions = [posn for (bin, posn) in self.aligned_positions]
return alignment_traceback(seqs, aligned_positions, word_length)
def getAlignment(self):
"""The alignment as a standard PyCogent Alignment object"""
seqs = self.pair_hmm.emission_probs.pair.getSeqNamePairs()
word_length = self.pair_hmm.emission_probs.pair.alphabet.getMotifLen()
aligned_positions = [posn for (bin, posn) in self.aligned_positions]
return alignment_traceback(seqs, aligned_positions, word_length)