def goldman_q_rna_pair(seq1, seq2):
"""Returns the Goldman rate matrix"""
if len(seq1) != len(seq2):
raise ValueError, "seq1 and seq2 are not the same length!"
seq1, seq2 = ModelRnaSequence(seq1), ModelRnaSequence(seq2)
m = Counts.fromPair(seq1, seq2, RnaPairs, average=True)._data
q = m / m.sum(axis=1)[:, NewAxis]
new_diag = -(q.sum(axis=1) - diag(q))
for i, v in enumerate(new_diag):
q[i, i] = v
return q
def goldman_q_rna_triple(seq1, seq2, outgroup):
"""Returns the Goldman rate matrix for seq1"""
if len(seq1) != len(seq2) != len(outgroup):
raise ValueError, "seq1,seq2 and outgroup are not the same length!"
seq1 = ModelRnaSequence(seq1)
seq2 = ModelRnaSequence(seq2)
outgroup = ModelRnaSequence(outgroup)
m = Counts.fromTriple(seq1, seq2, outgroup, RnaPairs)._data
q = m / m.sum(axis=1)[:, NewAxis]
new_diag = -(q.sum(axis=1) - diag(q))
for i, v in enumerate(new_diag):
q[i, i] = v
return q