clean up of chrom definitions

popsim-consortium · Jan 13, 2025 · c2f14c8 · c2f14c8
1 parent 35b8c71
commit c2f14c8
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Showing 3 changed files with 1 addition and 47 deletions.
diff --git a/stdpopsim/catalog/BosTau/species.py b/stdpopsim/catalog/BosTau/species.py
@@ -76,20 +76,6 @@
 _ploidy = {str(i): _species_ploidy for i in range(1, 30)}
 _ploidy.update({"X": _species_ploidy, "MT": 1})
 
-_chromosomes = []
-for name, data in genome_data.data["chromosomes"].items():
-    _chromosomes.append(
-        stdpopsim.Chromosome(
-            id=name,
-            length=data["length"],
-            synonyms=data["synonyms"],
-            # Harland et al. (2017), sex-averaged estimate per bp per generation.
-            mutation_rate=1.2e-8,
-            recombination_rate=_recombination_rate_data[name],
-            ploidy=_ploidy[name],
-        )
-    )
-
 _genome = stdpopsim.Genome.from_data(
     genome_data=genome_data.data,
     recombination_rate=_recombination_rate_data,

diff --git a/stdpopsim/catalog/CaeEle/species.py b/stdpopsim/catalog/CaeEle/species.py
@@ -106,23 +106,6 @@
     "MtDNA": 1,
 }
 
-_chromosomes = []
-for name, data in genome_data.data["chromosomes"].items():
-    _chromosomes.append(
-        stdpopsim.Chromosome(
-            id=name,
-            length=data["length"],
-            synonyms=data["synonyms"],
-            mutation_rate=_mutation_rate_data[name],
-            # _Konrad et al. de-nove mutation rate,
-            # it's not uniform and it's much better to use
-            # a mutation map.
-            # mutation_rate=_mutation_rate_data[name],
-            recombination_rate=_recombination_rate_data[name],
-            ploidy=_ploidy[name],
-        )
-    )
-
 _genome = stdpopsim.Genome.from_data(
     genome_data=genome_data.data,
     recombination_rate=_recombination_rate_data,

diff --git a/stdpopsim/catalog/CanFam/species.py b/stdpopsim/catalog/CanFam/species.py
@@ -97,9 +97,7 @@
 
 _mutation_rate = 4e-9
 _mutation_rate_data = {str(i): _mutation_rate for i in range(1, 39)}
-_mutation_rate_data["MT"] = (
-    _mutation_rate  
-)
+_mutation_rate_data["MT"] = _mutation_rate
 _mutation_rate_data["X"] = _mutation_rate
 
 _LindbladTohEtAl = stdpopsim.Citation(
@@ -133,19 +131,6 @@
     doi="https://doi.org/10.1534/g3.116.034678",
 )
 
-_chromosomes = []
-for name, data in genome_data.data["chromosomes"].items():
-    _chromosomes.append(
-        stdpopsim.Chromosome(
-            id=name,
-            length=data["length"],
-            synonyms=data["synonyms"],
-            mutation_rate=4e-9,  # based on non-CpG sites only
-            recombination_rate=_recombination_rate_data[name],
-            ploidy=_ploidy[name],
-        )
-    )
-
 _genome = stdpopsim.Genome.from_data(
     genome_data=genome_data.data,
     recombination_rate=_recombination_rate_data,