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