From a2564cc6ac6ce781e24aa129ff7a8aab74db7071 Mon Sep 17 00:00:00 2001
From: Peter Fields <peter.fields@jax.org>
Date: Sat, 4 Nov 2023 21:52:07 -0400
Subject: [PATCH] re-create genetic_maps.py file, add line to init

---
 stdpopsim/catalog/MusMus/__init__.py     |  1 +
 stdpopsim/catalog/MusMus/genetic_maps.py | 31 ++++++++++++++++++++++++
 2 files changed, 32 insertions(+)
 create mode 100644 stdpopsim/catalog/MusMus/genetic_maps.py

diff --git a/stdpopsim/catalog/MusMus/__init__.py b/stdpopsim/catalog/MusMus/__init__.py
index 8245a508e..9944bd93b 100644
--- a/stdpopsim/catalog/MusMus/__init__.py
+++ b/stdpopsim/catalog/MusMus/__init__.py
@@ -5,3 +5,4 @@
 from . import species  # noqa: F401
 from . import demographic_models  # noqa: F401
 from . import dfes  # noqa: F401
+from . import genetic_maps  # noqa: F401
diff --git a/stdpopsim/catalog/MusMus/genetic_maps.py b/stdpopsim/catalog/MusMus/genetic_maps.py
new file mode 100644
index 000000000..e106711af
--- /dev/null
+++ b/stdpopsim/catalog/MusMus/genetic_maps.py
@@ -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)