diff --git a/stdpopsim/catalog/HomSap/dfes.py b/stdpopsim/catalog/HomSap/dfes.py index de380172a..592e714b9 100644 --- a/stdpopsim/catalog/HomSap/dfes.py +++ b/stdpopsim/catalog/HomSap/dfes.py @@ -1,4 +1,4 @@ -import math +caimport math import stdpopsim _species = stdpopsim.get_species("HomSap") @@ -150,7 +150,7 @@ def _HuberLogNormalDFE(): def _KyriazisDFE(): - id = "GammaPlus_K23" # *** is Gamma specific enough? + id = "Mixed_K23" description = "Deleterious Gamma DFE with additional lethals" long_description = """ Return neutral and negative MutationType()s representing a human DFE. @@ -174,17 +174,19 @@ def _KyriazisDFE(): gamma_mean = 0.0131 gamma_shape = 0.186 coeffs = [0.45, 0.2, 0.05, 0] - breaks = [0.001, 0.01, 0.1, 1] + breaks = [0.001, 0.01, 0.1] gamma = stdpopsim.MutationType( dominance_coeff_list = coefs, dominance_coeff_breaks = breaks, distribution_type="g", # gamma distribution distribution_args=[gamma_mean, gamma_shape], ) + h=0 + s=1 lethal = stdpopsim.MutationType( - dominance_coeff_list = coefs, - dominance_coeff_breaks = breaks, - <> = 1 ## ******* + distribution_type="f", # fixed value + distribution_args=[-1], + dominance_coeff=h, ) # To get 0.63 deleterious mutations per 30Mb diploid coding sequence with # mu=1.29e-8 (current mu from catalog), we need a deleterious proportion