added Aedes aegypti

stdpopsim/catalog/AedAeg/__init__.py

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

stdpopsim/catalog/AedAeg/genome_data.py

@@ -0,0 +1,11 @@
+# File autogenerated from Ensembl REST API. Do not edit.
+data = {
+    "assembly_accession": "GCA_002204515.1",
+    "assembly_name": "AaegL5",
+    "chromosomes": {
+        "1": {"length": 310827022, "synonyms": []},
+        "2": {"length": 474425716, "synonyms": []},
+        "3": {"length": 409777670, "synonyms": []},
+        "MT": {"length": 16790, "synonyms": []},
+    },
+}

stdpopsim/catalog/AedAeg/species.py

@@ -0,0 +1,69 @@
+import stdpopsim
+
+from . import genome_data
+
+# These are in Table 1 of Juneja et al:
+_recombination_rate = {"1": 0.306, "2": 0.249, "3": 0.291, "MT": 0}
+
+_JunejaEtAl = stdpopsim.Citation(
+    doi="https://doi:10.1371/journal.pntd.0002652",
+    year=2014,
+    author="Juneja et al.",
+    reasons={stdpopsim.CiteReason.REC_RATE},
+)
+
+# This rate is for Drosophila (same as used in the A. gambiae tutorial).
+_overall_rate = 5.49e-9
+_mutation_rate = {
+    "1": _overall_rate,
+    "2": _overall_rate,
+    "3": _overall_rate,
+    "MT": _overall_rate,
+}
+
+_Ag1000G = stdpopsim.Citation(
+    doi="https://doi.org/10.1038/nature24995",
+    year=2017,
+    author="Ag1000G Consortium",
+    reasons={stdpopsim.CiteReason.MUT_RATE},
+)
+
+_NeneEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1126/science.1138878",
+    year=2007,
+    author="Nene et al.",
+    reasons={stdpopsim.CiteReason.ASSEMBLY},
+)
+
+
+_genome = stdpopsim.Genome.from_data(
+    genome_data.data,
+    recombination_rate=_recombination_rate,
+    mutation_rate=_mutation_rate,
+    citations=[
+        _NeneEtAl,
+        _Ag1000G,
+        _JunejaEtAl,
+    ],
+)
+
+
+_CrawfordEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1186/s12915-017-0351-0",
+    year=2017,
+    author="Crawford et al.",
+    reasons={stdpopsim.CiteReason.GEN_TIME, stdpopsim.CiteReason.POP_SIZE},
+)
+
+_species = stdpopsim.Species(
+    id="AedAeg",
+    ensembl_id="aedes_aegypti_lvpagwg",
+    name="Aedes aegypti",
+    common_name="Aedes aegypti (LVP_AGWG)",
+    genome=_genome,
+    generation_time=1 / 10,
+    population_size=1e6,
+    citations=[_CrawfordEtAl],
+)
+
+stdpopsim.register_species(_species)

tests/test_AedAeg.py

@@ -0,0 +1,49 @@
+import pytest
+
+import stdpopsim
+from tests import test_species
+
+
+class TestSpeciesData(test_species.SpeciesTestBase):
+
+    species = stdpopsim.get_species("AedAeg")
+
+    def test_ensembl_id(self):
+        assert self.species.ensembl_id == "aedes_aegypti_lvpagwg"
+
+    def test_name(self):
+        assert self.species.name == "Aedes aegypti"
+
+    def test_common_name(self):
+        assert self.species.common_name == "Aedes aegypti (LVP_AGWG)"
+
+    # 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("AedAeg").genome
+
+    @pytest.mark.skip("Recombination rate QC not done yet")
+    @pytest.mark.parametrize(
+        ["name", "rate"], {"1": -1, "2": -1, "3": -1, "MT": -1}.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"], {"1": -1, "2": -1, "3": -1, "MT": -1}.items()
+    )
+    def test_mutation_rate(self, name, rate):
+        assert pytest.approx(rate, self.genome.get_chromosome(name).mutation_rate)