Esempio n. 1
0
 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
Esempio n. 2
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 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