def get_distn(cls,
log_counts, codon_distn,
ts, tv, syn, nonsyn, compo, asym_compo,
natural_theta,
):
cls.check_theta(natural_theta)
nt_distn = markovutil.ratios_to_distn(natural_theta[2:5])
codon_distn = codon1994.get_f1x4_codon_distn(compo, nt_distn)
return codon_distn
def get_pre_Q(cls,
log_counts, codon_distn,
ts, tv, syn, nonsyn, compo, asym_compo,
natural_theta,
):
cls.check_theta(theta)
kappa = natural_theta[0]
omega = natural_theta[1]
nt_distn = markovutil.ratios_to_distn(theta[2:5])
codon_distn = codon1994.get_f1x4_codon_distn(compo, nt_distn)
pre_Q = codon1994.get_pre_Q(
ts, tv, syn, nonsyn,
codon_distn, kappa, omega)
return pre_Q