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fixed pre-commit checks
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chriscrsmith committed Nov 9, 2021
1 parent 5c47d10 commit f2a6d89
Showing 1 changed file with 11 additions and 17 deletions.
28 changes: 11 additions & 17 deletions stdpopsim/catalog/HomSap/dfes.py
Expand Up @@ -47,17 +47,15 @@ def _KimDFE():
_species.add_dfe(_KimDFE())




def _HuberDFE():
id = "Gamma_H17"
id = "Gamma_H17"
description = "Deleterious Gamma DFE"
long_description = """
Return neutral and negative MutationType()s representing a Homo sapiens DFE.
Huber et al. (2017), https://doi.org/10.1073/pnas.1619508114.
DFE parameters are based on the Full Model described in Table S2, in which
All Data (none of the listed filters) were used.
""" # [this was a different filtering scheme than the Huber et al DroMel DFE ]
All Data (none of the listed filters) were used.
""" # [this was a different filtering scheme than the Huber et al DroMel DFE ]
citations = [
stdpopsim.Citation(
author="Huber et al.",
Expand All @@ -68,30 +66,26 @@ def _HuberDFE():
]
neutral = stdpopsim.MutationType()
gamma_shape = 0.19 # shape
gamma_mean = -0.014 # expected value
gamma_mean = -0.014 # 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=[0.3, 0.7], # [0.3 and 0.7 were used in Xin's analysis, but I couldn't find these values in the Huber paper]
proportions=[
0.3,
0.7,
], # [0.3 and 0.7 were used in Xin's analysis,
# but I couldn't find these values in the Huber paper]
citations=citations,
)


_species.add_dfe(_HuberDFE())








_species.add_dfe(_HuberDFE())

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