From da41e3069f382a8b9392bc314c8115dc09cf8a24 Mon Sep 17 00:00:00 2001 From: peterdfields Date: Thu, 21 Mar 2024 16:55:22 -0400 Subject: [PATCH 1/4] add dfes.py configuration file --- stdpopsim/catalog/MusMus/dfes.py | 51 ++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 stdpopsim/catalog/MusMus/dfes.py diff --git a/stdpopsim/catalog/MusMus/dfes.py b/stdpopsim/catalog/MusMus/dfes.py new file mode 100644 index 000000000..ad201badc --- /dev/null +++ b/stdpopsim/catalog/MusMus/dfes.py @@ -0,0 +1,51 @@ +import stdpopsim + +_species = stdpopsim.get_species("MusMus") + +########################################################### +# +# DFEs +# +########################################################### + + +def _BookerDFE(): + id = "Gamma_Booker2021_CDS" + 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=[0.333, 0.664], + citations=citations, + ) + + +_species.add_dfe(_BookerDFE()) From 108f40eceea88f2cb778037c1a529a808a89b4f6 Mon Sep 17 00:00:00 2001 From: peterdfields Date: Tue, 26 Mar 2024 20:12:12 -0400 Subject: [PATCH 2/4] add line to init importing dfe --- stdpopsim/catalog/MusMus/__init__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/stdpopsim/catalog/MusMus/__init__.py b/stdpopsim/catalog/MusMus/__init__.py index 844fb86de..cef5118dd 100644 --- a/stdpopsim/catalog/MusMus/__init__.py +++ b/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 From 2dd9b0d5c845860b67de4d7994a3e7fde2371f41 Mon Sep 17 00:00:00 2001 From: peterdfields Date: Tue, 26 Mar 2024 20:16:59 -0400 Subject: [PATCH 3/4] fix neutral,non-neutral props. --- stdpopsim/catalog/MusMus/dfes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stdpopsim/catalog/MusMus/dfes.py b/stdpopsim/catalog/MusMus/dfes.py index ad201badc..17277c518 100644 --- a/stdpopsim/catalog/MusMus/dfes.py +++ b/stdpopsim/catalog/MusMus/dfes.py @@ -43,7 +43,7 @@ def _BookerDFE(): description=description, long_description=long_description, mutation_types=[neutral, negative], - proportions=[0.333, 0.664], + proportions=[0.334, 0.666], citations=citations, ) From 82af0860557effbb7e257bac0819ce381408e246 Mon Sep 17 00:00:00 2001 From: peterdfields Date: Tue, 26 Mar 2024 20:31:40 -0400 Subject: [PATCH 4/4] try shorter dfe model name --- stdpopsim/catalog/MusMus/dfes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stdpopsim/catalog/MusMus/dfes.py b/stdpopsim/catalog/MusMus/dfes.py index 17277c518..f153d1530 100644 --- a/stdpopsim/catalog/MusMus/dfes.py +++ b/stdpopsim/catalog/MusMus/dfes.py @@ -10,7 +10,7 @@ def _BookerDFE(): - id = "Gamma_Booker2021_CDS" + id = "Gamma_B21" description = "Deleterious Gamma DFE CDS" long_description = """ Return negative MutationType()s representing a Mus