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added stickleback genome and fixed common name
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""" | ||
Catalog definitions for GasAcu (Ensembl ID='9307941') | ||
""" | ||
from . import species # noqa: F401 |
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# File autogenerated from Ensembl REST API. Do not edit. | ||
data = { | ||
"assembly_accession": "GCF_016920845.1", | ||
"assembly_name": "GAculeatus_UGA_version5", | ||
"chromosomes": { | ||
"1": {"length": 29619991, "synonyms": []}, | ||
"2": {"length": 23686546, "synonyms": []}, | ||
"3": {"length": 17759012, "synonyms": []}, | ||
"4": {"length": 34181212, "synonyms": []}, | ||
"5": {"length": 15550311, "synonyms": []}, | ||
"6": {"length": 18825451, "synonyms": []}, | ||
"7": {"length": 30776923, "synonyms": []}, | ||
"8": {"length": 20553084, "synonyms": []}, | ||
"9": {"length": 20843631, "synonyms": []}, | ||
"10": {"length": 17985176, "synonyms": []}, | ||
"11": {"length": 17651971, "synonyms": []}, | ||
"12": {"length": 20694444, "synonyms": []}, | ||
"13": {"length": 20748428, "synonyms": []}, | ||
"14": {"length": 16147532, "synonyms": []}, | ||
"15": {"length": 17318724, "synonyms": []}, | ||
"16": {"length": 19507025, "synonyms": []}, | ||
"17": {"length": 20195758, "synonyms": []}, | ||
"18": {"length": 15939336, "synonyms": []}, | ||
"19": {"length": 20580295, "synonyms": []}, | ||
"20": {"length": 20445003, "synonyms": []}, | ||
"21": {"length": 17421465, "synonyms": []}, | ||
"Y": {"length": 15859692, "synonyms": []}, | ||
"MT": {"length": 16543, "synonyms": []}, | ||
}, | ||
} |
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import stdpopsim | ||
|
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from . import genome_data | ||
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_recombination_rate = { | ||
"1": 3.11e-08, | ||
"2": 3.11e-08, | ||
"3": 3.11e-08, | ||
"4": 3.11e-08, | ||
"5": 3.11e-08, | ||
"6": 3.11e-08, | ||
"7": 3.11e-08, | ||
"8": 3.11e-08, | ||
"9": 3.11e-08, | ||
"10": 3.11e-08, | ||
"11": 3.11e-08, | ||
"12": 3.11e-08, | ||
"13": 3.11e-08, | ||
"14": 3.11e-08, | ||
"15": 3.11e-08, | ||
"16": 3.11e-08, | ||
"17": 3.11e-08, | ||
"18": 3.11e-08, | ||
"19": 3.11e-08, | ||
"20": 3.11e-08, | ||
"21": 3.11e-08, | ||
"Y": 0, | ||
"MT": 0, | ||
} | ||
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_overall_rate = 3.7e-8 | ||
_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, | ||
"Y": _overall_rate, | ||
"MT": _overall_rate, | ||
} | ||
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_genome = stdpopsim.Genome.from_data( | ||
genome_data.data, | ||
recombination_rate=_recombination_rate, | ||
mutation_rate=_mutation_rate, | ||
citations=[ | ||
stdpopsim.Citation( | ||
author="Peichel et al.", | ||
year=2017, | ||
doi="https://doi.org/10.1093/jhered/esx058", | ||
reasons={stdpopsim.CiteReason.ASSEMBLY}, | ||
), | ||
stdpopsim.Citation( | ||
author="Roesti et al.", | ||
year=2013, | ||
doi="https://10.1111/mec.12322", | ||
reasons={stdpopsim.CiteReason.REC_RATE}, | ||
), | ||
stdpopsim.Citation( | ||
author="Liu et al.", | ||
year=2016, | ||
doi="https://10.1111/mec.13827", | ||
reasons={stdpopsim.CiteReason.MUT_RATE}, | ||
), | ||
], | ||
) | ||
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_species = stdpopsim.Species( | ||
id="GasAcu", | ||
ensembl_id="9307941", | ||
name="Gasterosteus aculeatus", | ||
common_name="Three-spined stickleback", | ||
genome=_genome, | ||
generation_time=1, | ||
population_size=1e4, | ||
citations=[ | ||
stdpopsim.Citation( | ||
author="Liu et al.", | ||
year=2016, | ||
doi="https://10.1111/mec.13827", | ||
reasons={stdpopsim.CiteReason.POP_SIZE, stdpopsim.CiteReason.GEN_TIME}, | ||
), | ||
], | ||
) | ||
|
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stdpopsim.register_species(_species) |
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import pytest | ||
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import stdpopsim | ||
from tests import test_species | ||
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class TestSpeciesData(test_species.SpeciesTestBase): | ||
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species = stdpopsim.get_species("GasAcu") | ||
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def test_ensembl_id(self): | ||
assert self.species.ensembl_id == "9307941" | ||
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def test_name(self): | ||
assert self.species.name == "Gasterosteus aculeatus" | ||
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def test_common_name(self): | ||
assert self.species.common_name == "Three-spined stickleback" | ||
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# 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 | ||
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@pytest.mark.skip("Generation time QC not done yet") | ||
def test_qc_generation_time(self): | ||
assert self.species.generation_time == -1 | ||
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class TestGenomeData(test_species.GenomeTestBase): | ||
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genome = stdpopsim.get_species("GasAcu").genome | ||
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@pytest.mark.skip("Recombination rate QC not done yet") | ||
@pytest.mark.parametrize( | ||
["name", "rate"], | ||
{ | ||
"1": -1, | ||
"2": -1, | ||
"3": -1, | ||
"4": -1, | ||
"5": -1, | ||
"6": -1, | ||
"7": -1, | ||
"8": -1, | ||
"9": -1, | ||
"10": -1, | ||
"11": -1, | ||
"12": -1, | ||
"13": -1, | ||
"14": -1, | ||
"15": -1, | ||
"16": -1, | ||
"17": -1, | ||
"18": -1, | ||
"19": -1, | ||
"20": -1, | ||
"21": -1, | ||
"Y": -1, | ||
"MT": -1, | ||
}.items(), | ||
) | ||
def test_recombination_rate(self, name, rate): | ||
assert rate == pytest.approx( | ||
self.genome.get_chromosome(name).recombination_rate | ||
) | ||
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@pytest.mark.skip("Mutation rate QC not done yet") | ||
@pytest.mark.parametrize( | ||
["name", "rate"], | ||
{ | ||
"1": -1, | ||
"2": -1, | ||
"3": -1, | ||
"4": -1, | ||
"5": -1, | ||
"6": -1, | ||
"7": -1, | ||
"8": -1, | ||
"9": -1, | ||
"10": -1, | ||
"11": -1, | ||
"12": -1, | ||
"13": -1, | ||
"14": -1, | ||
"15": -1, | ||
"16": -1, | ||
"17": -1, | ||
"18": -1, | ||
"19": -1, | ||
"20": -1, | ||
"21": -1, | ||
"Y": -1, | ||
"MT": -1, | ||
}.items(), | ||
) | ||
def test_mutation_rate(self, name, rate): | ||
assert rate == pytest.approx(self.genome.get_chromosome(name).mutation_rate) |