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