Getting started with DFE for MusMus

stdpopsim/catalog/MusMus/__init__.py

@@ -3,3 +3,4 @@
 """
 from . import species  # noqa: F401
 from . import demographic_models  # noqa: F401
+from . import dfes  # noqa: F401

stdpopsim/catalog/MusMus/dfes.py

@@ -0,0 +1,51 @@
+import stdpopsim
+
+_species = stdpopsim.get_species("MusMus")
+
+###########################################################
+#
+# DFEs
+#
+###########################################################
+
+
+def _BookerDFE():
+    id = "Gamma_B21"
+    description = "Deleterious Gamma DFE CDS"
+    long_description = """
+    Return negative MutationType()s representing a Mus
+    musculus subsp. castaneous DFE for protein coded exons or CDS. Booker et al. (2021),
+    https://doi.org/10.1101/2021.06.10.447924
+    DFE parameters are based on an analysis of the unfolded site frequency spectrum
+    (uSFS) using polyDFE v2 (Tataru and Bataillon 2019) as presented in Booker
+    et al. (2021).
+    """
+    citations = [
+        stdpopsim.Citation(
+            author="Booker et al.",
+            year=2021,
+            doi="https://doi.org/10.1101/2021.06.10.447924",
+            reasons={stdpopsim.CiteReason.DFE},  # include the dfe_model reason
+        )
+    ]
+    neutral = stdpopsim.MutationType()
+    gamma_shape = 0.186  # shape
+    gamma_mean = -5.96e-02  # expected value
+    h = 0.5  # dominance coefficient
+    negative = stdpopsim.MutationType(
+        dominance_coeff=h,
+        distribution_type="g",  # gamma distribution
+        distribution_args=[gamma_mean, gamma_shape],
+    )
+
+    return stdpopsim.DFE(
+        id=id,
+        description=description,
+        long_description=long_description,
+        mutation_types=[neutral, negative],
+        proportions=[0.334, 0.666],
+        citations=citations,
+    )
+
+
+_species.add_dfe(_BookerDFE())