def get_distn(cls,
log_counts, codon_distn,
ts, tv, syn, nonsyn, compo, asym_compo,
theta,
):
cls.check_theta(theta)
nt_distn = markovutil.log_ratios_to_distn(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,
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
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 = fmutsel.get_pre_Q(
log_counts,
fmutsel.preferred_recessive_fixation,
ts, tv, syn, nonsyn, compo, asym_compo,
nt_distn, kappa, omega,
)
return pre_Q
