def _align_pairwise(s1,
s2,
mprobs,
psub,
TM,
local,
return_alignment=True,
return_score=False,
**kw):
"""Generic alignment with any substitution model and indel model"""
[p1, p2] = [make_likelihood_tree_leaf(seq) for seq in [s1, s2]]
[p1, p2] = [pairwise.AlignableSeq(leaf) for leaf in [p1, p2]]
pair = pairwise.Pair(p1, p2)
EP = pair.make_simple_emission_probs(mprobs, [psub])
hmm = EP.make_pair_HMM(TM)
vpath = hmm.get_viterbi_path(local=local, **kw)
score = vpath.get_score()
if return_alignment:
alignment = vpath.get_alignment()
if return_score:
return (alignment, score)
else:
return alignment
else:
return score
def Edge(seq1, seq2, length, bin_data, switch=1.0, bprobs=None):
# one sequence pair in, potentialy, a tree
bins = len(bin_data)
pair = pairwise.Pair(seq1, seq2)
EP = pair.make_reversible_emission_probs([(bin.mprobs, bin.Qd)
for bin in bin_data], length)
tms = [bin.indel.calc_transition_matrix(length) for bin in bin_data]
if bins == 1:
TM = tms[0]
else:
assert bprobs
R = SiteClassTransitionMatrix(switch, bprobs)
TM = R.nestTransitionMatricies(tms)
assert min(TM.Matrix.flat) >= 0, bin_data
return EP.make_pair_HMM(TM)
