Merge pull request #872 from jradrion/drosec

added drosophila sechellia

stdpopsim/catalog/DroSec/__init__.py

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

stdpopsim/catalog/DroSec/genome_data.py

@@ -0,0 +1,13 @@
+# File created manually from https://www.ncbi.nlm.nih.gov/assembly/GCF_004382195.1
+data = {
+    "assembly_accession": "GCA_004382195.1",
+    "assembly_name": "ASM438219v1",
+    "chromosomes": {
+        "2L": {"length": 24956976, "synonyms": []},
+        "2R": {"length": 21536224, "synonyms": []},
+        "3L": {"length": 28131630, "synonyms": []},
+        "3R": {"length": 30464902, "synonyms": []},
+        "X": {"length": 22909512, "synonyms": []},
+        "4": {"length": 1277805, "synonyms": []},
+    },
+}

stdpopsim/catalog/DroSec/species.py

@@ -0,0 +1,88 @@
+import stdpopsim
+
+from . import genome_data
+
+_ChakrabortyEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1101/gr.263442.120",
+    year=2021,
+    author="Chakraborty et al.",
+    reasons={stdpopsim.CiteReason.ASSEMBLY},
+)
+
+_ComeronEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1371/journal.pgen.1002905",
+    year=2012,
+    author="Comeron et al.",
+    reasons={stdpopsim.CiteReason.REC_RATE},
+)
+
+_LegrandEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1534/genetics.108.092080",
+    year=2009,
+    author="Legrand et al.",
+    reasons={
+        stdpopsim.CiteReason.GEN_TIME,
+        stdpopsim.CiteReason.MUT_RATE,
+        stdpopsim.CiteReason.POP_SIZE,
+    },
+)
+
+# We used recombination rates estimated in DroMel.
+# Mean chromosomal rates, calculated from the Comeron 2012 map.
+# Chromosome 4 isn't in this map, so the weighted mean of 2L, 2R, 3L and 3R
+# was used instead.
+_recombination_rate = {
+    "2L": 2.4125016027908946e-08,
+    "2R": 2.2366522822806982e-08,
+    "3L": 1.7985794693631893e-08,
+    "3R": 1.7165556232922828e-08,
+    "X": 2.9151053903465754e-08,
+    "4": 2.0085234464525437e-08,
+}
+
+# Mutation rate is set to that used by
+# Legrand et al. in an ABC selection of
+# demographic scenarios (page 1200).
+# They state this is an estimate taken
+# from D. simulans (Wall et al. 2002).
+_overall_rate = 1.5e-9
+_mutation_rate = {
+    "2L": _overall_rate,
+    "2R": _overall_rate,
+    "3L": _overall_rate,
+    "3R": _overall_rate,
+    "X": _overall_rate,
+    "4": _overall_rate,
+}
+
+# We could not auto-pull the genome data from ensemble
+# so instead we used the most up-to-date assembly
+# currently available from NCBI.
+_genome = stdpopsim.Genome.from_data(
+    genome_data.data,
+    recombination_rate=_recombination_rate,
+    mutation_rate=_mutation_rate,
+    citations=[
+        _ChakrabortyEtAl,
+        _ComeronEtAl,
+        _LegrandEtAl,
+    ],
+)
+
+
+# Generation time was set to that used by
+# by Legrand et al. in an ABC selection of demographic
+# scenarios (page 1200).
+# Population size was estimated in the same paper (page 1202).
+_species = stdpopsim.Species(
+    id="DroSec",
+    ensembl_id="drosophila_sechellia",
+    name="Drosophila sechellia",
+    common_name="Drosophila sechellia",
+    genome=_genome,
+    generation_time=0.05,
+    population_size=100000,
+    citations=[_LegrandEtAl],
+)
+
+stdpopsim.register_species(_species)

tests/test_DroSec.py

@@ -0,0 +1,45 @@
+import pytest
+
+import stdpopsim
+from tests import test_species
+
+
+class TestSpeciesData(test_species.SpeciesTestBase):
+
+    species = stdpopsim.get_species("DroSec")
+
+    def test_ensembl_id(self):
+        assert self.species.ensembl_id == "drosophila_sechellia"
+
+    def test_name(self):
+        assert self.species.name == "Drosophila sechellia"
+
+    def test_common_name(self):
+        assert self.species.common_name == "Drosophila sechellia"
+
+    # 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("DroSec").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)