Adding genetic map for honeybee

stdpopsim/catalog/ApiMel/__init__.py

@@ -2,3 +2,4 @@
 Catalog definitions for ApiMel (Ensembl ID='apis_mellifera')
 """
 from . import species  # noqa: F401
+from . import genetic_maps  # noqa: F401

stdpopsim/catalog/ApiMel/genetic_maps.py

@@ -0,0 +1,35 @@
+import stdpopsim
+
+_species = stdpopsim.get_species("ApiMel")
+
+_genetic_map_citation = stdpopsim.Citation(
+    doi="https://doi.org/10.1186/s13059-014-0566-0",
+    author="Liu et al.",
+    year=2015,
+    reasons={stdpopsim.CiteReason.GEN_MAP},
+)
+
+_gm = stdpopsim.GeneticMap(
+    species=_species,
+    id="Liu_Amel_HAv3.1",  # ID for genetic map, see naming conventions
+    description="Crossover events mapped in 55 individuals",
+    long_description="""
+        This map is based on the study of crossover events in 55 individuals
+        from three colonies of Apis mellifera ligustica from China. The study
+        included three diploid queens, six diploid workers, and 46 haploid
+        drones. The map was first lifted from the Amel_4.5 to Amel_HAv3.1
+        assembly. To convert the crossover events to genetic position, the
+        recombination rate was assumed stable between crossovers and the
+        genetic position was inferred from the physical positions of SNPs
+        within these crossover ranges.
+        """,
+    url=(
+        "https://stdpopsim.s3.us-west-2.amazonaws.com/"
+        "genetic_maps/ApiMel/Liu2015_liftover_maps.tar.gz"
+    ),
+    sha256="fb394ca952324224c1adc1a5c64ed0117d260baabb21520409f4c3621ea5c649",
+    file_pattern="Liu2015_liftover_maps/Amel_HAv3.1_lifted_chr{id}.txt",
+    citations=[_genetic_map_citation],
+)
+
+_species.add_genetic_map(_gm)