def get_mixture(cls,
log_counts, codon_distn,
ts, tv, syn, nonsyn, compo, asym_compo,
natural_theta,
):
"""
@return: finite_distn, pre_Q_matrices
"""
cls.check_theta(natural_theta)
p0 = natural_theta[0]
p1 = 1 - p0
first_omega = natural_theta[1]
second_omega = natural_theta[2]
kappa = natural_theta[3]
nt_distn = markovutil.ratios_to_distn(natural_theta[4:4+3])
first_pre_Q = fmutsel.get_pre_Q(
log_counts,
fmutsel.genic_fixation,
ts, tv, syn, nonsyn, compo, asym_compo,
nt_distn, kappa, first_omega,
)
second_pre_Q = fmutsel.get_pre_Q(
log_counts,
fmutsel.genic_fixation,
ts, tv, syn, nonsyn, compo, asym_compo,
nt_distn, kappa, second_omega,
)
return (p0, p1), (first_pre_Q, second_pre_Q)
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(natural_theta)
kimura_d = natural_theta[0]
kappa = natural_theta[1]
omega = natural_theta[2]
nt_distn = markovutil.ratios_to_distn(natural_theta[3:6])
pre_Q = fmutsel.get_pre_Q_unconstrained(
log_counts, ts, tv, syn, nonsyn, compo, asym_compo, kimura_d, nt_distn, kappa, omega
)
return pre_Q
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,
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 = fmutsel.get_pre_Q(
log_counts,
fmutsel.preferred_recessive_fixation,
ts, tv, syn, nonsyn, compo, 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,
natural_theta,
):
cls.check_theta(natural_theta)
first_proportion = natural_theta[0]
first_omega = natural_theta[1]
second_omega = natural_theta[2]
kappa = natural_theta[3]
nt_distn = markovutil.ratios_to_distn(natural_theta[4:4+3])
pre_Q = fmutsel.get_pre_Q(
log_counts,
fmutsel.genic_fixation,
ts, tv, syn, nonsyn, compo, asym_compo,
nt_distn, kappa, omega,
)
return pre_Q
def get_mixture(cls,
log_counts, codon_distn,
ts, tv, syn, nonsyn, compo, asym_compo,
natural_theta,
):
cls.check_theta(natural_theta)
p0 = natural_theta[0]
p1 = 1 - p0
first_omega = natural_theta[1]
second_omega = natural_theta[2]
kimura_d = natural_theta[3]
kappa = natural_theta[4]
nt_distn = markovutil.ratios_to_distn(natural_theta[5:5+3])
first_pre_Q = fmutsel.get_pre_Q_unconstrained(
log_counts,
ts, tv, syn, nonsyn, compo, asym_compo,
kimura_d, nt_distn, kappa, first_omega,
)
second_pre_Q = fmutsel.get_pre_Q_unconstrained(
log_counts,
ts, tv, syn, nonsyn, compo, asym_compo,
kimura_d, nt_distn, kappa, second_omega,
)
return (p0, p1), (first_pre_Q, second_pre_Q)