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Mus mus Cox map, try two #1539

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1 change: 1 addition & 0 deletions stdpopsim/catalog/MusMus/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,4 @@
"""
from . import species # noqa: F401
from . import demographic_models # noqa: F401
from . import genetic_maps # noqa: F401
31 changes: 31 additions & 0 deletions stdpopsim/catalog/MusMus/genetic_maps.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
import stdpopsim

_species = stdpopsim.get_species("MusMus")

_genetic_map_citation = stdpopsim.Citation(
doi="https://doi.org/10.1534/genetics.109.105486",
author="Cox et al.",
year=2009,
reasons={stdpopsim.CiteReason.GEN_MAP},
)

_gm = stdpopsim.GeneticMap(
species=_species,
id="Cox_etal_2009_v3_GRCm39", # ID for genetic map, see naming conventions
description="Revised Cox genetic map, for mouse genome build 39 coordinates",
long_description="""
This map results from the Cox et al. (2009) genetic map which has been
lifted over to the GRCm39 genome which was released in 2020. As described in
the abstract of Cox et al. (2009), the genetic map resulted from a large
heterogeneous mouse population and incorporates 10,195 SNPs using a set
of 47 families comprising 3546 meioses. The methods by which this original
map was lifted to the GRCm39 genome are described on a github repo:
https://github.com/kbroman/CoxMapV3
""",
url=("https://stdpopsim.s3-us-west-2.amazonaws.com/genetic_maps/dir/cox.tar.gz"),
sha256="d589a7adf334f31343aff722aeebe96b1663cab573856d80a883f07bd3cb9b11",
file_pattern="Cox_etal_2009_v3_GRCm39_{id}.txt",
citations=[_genetic_map_citation],
)

_species.add_genetic_map(_gm)
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