added Heliconius melpomene

stdpopsim/catalog/HelMel/__init__.py

@@ -0,0 +1,4 @@
+"""
+Catalog definitions for HelMel (Ensembl ID='heliconius_melpomene')
+"""
+from . import species  # noqa: F401

stdpopsim/catalog/HelMel/genome_data.py

@@ -0,0 +1,35 @@
+# File autogenerated from Ensembl REST API. Do not edit.
+#
+# Manually edited. See
+# https://github.com/popsim-consortium/stdpopsim/issues/835#issuecomment-815854055
+#
+# Data source:
+# http://ensembl.lepbase.org/Heliconius_melpomene_melpomene_hmel25/Info/Index
+#
+data = {
+    "assembly_accession": None,  # No accession number available
+    "assembly_name": "Hmel2.5",
+    "chromosomes": {
+        "1": {"length": 17206585, "synonyms": []},
+        "2": {"length": 9045316, "synonyms": []},
+        "3": {"length": 10541528, "synonyms": []},
+        "4": {"length": 9662098, "synonyms": []},
+        "5": {"length": 9908586, "synonyms": []},
+        "6": {"length": 1405417, "synonyms": []},
+        "7": {"length": 1430885, "synonyms": []},
+        "8": {"length": 9320449, "synonyms": []},
+        "9": {"length": 8708747, "synonyms": []},
+        "10": {"length": 1796548, "synonyms": []},
+        "11": {"length": 1175927, "synonyms": []},
+        "12": {"length": 1632729, "synonyms": []},
+        "13": {"length": 1812731, "synonyms": []},
+        "14": {"length": 9174305, "synonyms": []},
+        "15": {"length": 1023575, "synonyms": []},
+        "16": {"length": 1008321, "synonyms": []},
+        "17": {"length": 1477329, "synonyms": []},
+        "18": {"length": 1680389, "synonyms": []},
+        "19": {"length": 1639934, "synonyms": []},
+        "20": {"length": 1487169, "synonyms": []},
+        "21": {"length": 1335969, "synonyms": []},
+    },
+}

stdpopsim/catalog/HelMel/species.py

@@ -0,0 +1,92 @@
+import stdpopsim
+
+from . import genome_data
+
+_recombination_rate = {
+    "1": 3.17e-8,
+    "2": 5.61e-8,
+    "3": 5.10e-8,
+    "4": 4.97e-8,
+    "5": 5.15e-8,
+    "6": 3.40e-8,
+    "7": 3.76e-8,
+    "8": 5.28e-8,
+    "9": 5.31e-8,
+    "10": 3.16e-8,
+    "11": 4.47e-8,
+    "12": 3.13e-8,
+    "13": 3.08e-8,
+    "14": 5.47e-8,
+    "15": 4.78e-8,
+    "16": 4.71e-8,
+    "17": 3.94e-8,
+    "18": 3.16e-8,
+    "19": 3.11e-8,
+    "20": 3.45e-8,
+    "21": 3.71e-8,
+}
+
+_overall_rate = 2.9e-9
+_mutation_rate = {
+    "1": _overall_rate,
+    "2": _overall_rate,
+    "3": _overall_rate,
+    "4": _overall_rate,
+    "5": _overall_rate,
+    "6": _overall_rate,
+    "7": _overall_rate,
+    "8": _overall_rate,
+    "9": _overall_rate,
+    "10": _overall_rate,
+    "11": _overall_rate,
+    "12": _overall_rate,
+    "13": _overall_rate,
+    "14": _overall_rate,
+    "15": _overall_rate,
+    "16": _overall_rate,
+    "17": _overall_rate,
+    "18": _overall_rate,
+    "19": _overall_rate,
+    "20": _overall_rate,
+    "21": _overall_rate,
+}
+
+_genome = stdpopsim.Genome.from_data(
+    genome_data.data,
+    recombination_rate=_recombination_rate,
+    mutation_rate=_mutation_rate,
+    citations=[
+        stdpopsim.Citation(
+            author="Davey et al",
+            year=2017,
+            doi="https://doi.org/10.1002/evl3.12",
+            reasons={stdpopsim.CiteReason.ASSEMBLY, stdpopsim.CiteReason.REC_RATE},
+        ),
+        stdpopsim.Citation(
+            author="Keightley et al",
+            year=2015,
+            doi="https://doi.org/10.1093/molbev/msu302",
+            reasons={stdpopsim.CiteReason.MUT_RATE},
+        ),
+    ],
+)
+
+_species = stdpopsim.Species(
+    id="HelMel",
+    ensembl_id="heliconius_melpomene",
+    name="Heliconius melpomene",
+    common_name="Heliconius melpomene",
+    genome=_genome,
+    generation_time=9.5 / 100,
+    population_size=2.1e6,
+    citations=[
+        stdpopsim.Citation(
+            author="Pardo-Diaz et al",
+            year=2012,
+            doi="https://doi.org/10.1371/journal.pgen.1002752",
+            reasons={stdpopsim.CiteReason.POP_SIZE, stdpopsim.CiteReason.GEN_TIME},
+        ),
+    ],
+)
+
+stdpopsim.register_species(_species)

tests/test_HelMel.py

@@ -0,0 +1,45 @@
+import pytest
+
+import stdpopsim
+from tests import test_species
+
+
+class TestSpeciesData(test_species.SpeciesTestBase):
+
+    species = stdpopsim.get_species("HelMel")
+
+    def test_ensembl_id(self):
+        assert self.species.ensembl_id == "heliconius_melpomene"
+
+    def test_name(self):
+        assert self.species.name == "Heliconius melpomene"
+
+    def test_common_name(self):
+        assert self.species.common_name == "Heliconius melpomene"
+
+    # QC Tests. These tests are performed by another contributor
+    # independently referring to the citations provided in the
+    # species definition, filling in the appropriate values
+    # and deleting the pytest "skip" annotations.
+    @pytest.mark.skip("Population size QC not done yet")
+    def test_qc_population_size(self):
+        assert self.species.population_size == -1
+
+    @pytest.mark.skip("Generation time QC not done yet")
+    def test_qc_generation_time(self):
+        assert self.species.generation_time == -1
+
+
+class TestGenomeData(test_species.GenomeTestBase):
+
+    genome = stdpopsim.get_species("HelMel").genome
+
+    @pytest.mark.skip("Recombination rate QC not done yet")
+    @pytest.mark.parametrize(["name", "rate"], {}.items())
+    def test_recombination_rate(self, name, rate):
+        assert pytest.approx(rate, self.genome.get_chromosome(name).recombination_rate)
+
+    @pytest.mark.skip("Mutation rate QC not done yet")
+    @pytest.mark.parametrize(["name", "rate"], {}.items())
+    def test_mutation_rate(self, name, rate):
+        assert pytest.approx(rate, self.genome.get_chromosome(name).mutation_rate)