flake8

stdpopsim/catalog/HomSap/dfes.py

@@ -38,6 +38,7 @@ def _KimDFE():
     # in how fitness is defined
     # (1+s for homozygote in SLiM versus 1+2s in dadi)
     gamma_mean = (-gamma_shape * gamma_scale * 2) / (2 * Na)  # expected value
+    print(gamma_mean)
     h = 0.5  # dominance coefficient
     negative = stdpopsim.MutationType(
         dominance_coeff=h,
@@ -171,24 +172,24 @@ def _KyriazisDFE():
         )
     ]
     neutral = stdpopsim.MutationType()
-    gamma_mean = 0.0131
+    gamma_mean = -0.0131
     gamma_shape = 0.186
-    coefs = [0.45,  0.2,  0.05, 0]
+    coefs = [0.45, 0.2, 0.05, 0]
     breaks = [0.001, 0.01, 0.1]
     gamma = stdpopsim.MutationType(
-        dominance_coeff_list = coefs,
-        dominance_coeff_breaks = breaks,
+        dominance_coeff_list=coefs,
+        dominance_coeff_breaks=breaks,
         distribution_type="g",  # gamma distribution
         distribution_args=[gamma_mean, gamma_shape],
     )
-    h=0
-    s=1
+    h = 0
+    s = -1
     lethal = stdpopsim.MutationType(
-        distribution_type="f", # fixed value
-        distribution_args=[-1],
+        distribution_type="f",  # fixed value
+        distribution_args=[s],
         dominance_coeff=h,
-    )    
-    # To get 0.63 deleterious mutations per 30Mb diploid coding sequence using 
+    )
+    # To get 0.63 deleterious mutations per 30Mb diploid coding sequence using
     # mu from catalog, we need a deleterious proportion of:
     proportion_deleterious = 0.63 / (3e7 * _species.genome.mean_mutation_rate * 2)
 
@@ -208,4 +209,5 @@ def _KyriazisDFE():
         citations=citations,
     )
 
+
 _species.add_dfe(_KyriazisDFE())