_CampbellEtAl.because(stdpopsim.CiteReason.REC_RATE),
_LindbladTohEtAl.because(stdpopsim.CiteReason.ASSEMBLY),
],
)
_species = stdpopsim.Species(
id="CanFam",
ensembl_id="canis_familiaris",
name="Canis familiaris",
common_name="Dog",
genome=_genome,
population_size=13000, # ancestral dog size
generation_time=3,
citations=[
# Everyone uses 3 years for generation time because everyone else uses it.
# It's likely higher, at least in wolves:
# https://academic.oup.com/mbe/article/35/6/1366/4990884
# Reasoning behind a generation time of 3 years:
# Consider two use cases for CanFam simulations:
# (1) for domestic dog simulations, and (2) for wolf+dog simulations
# (or ancestral dogs).
# In case (1), maybe 3 year generations are more appropriate because of human
# intervention in breeding. In case (2), you might want to match what other
# studies have done (thus using 3 year generations), or you might want to
# consider what is known about modern wolves.
_LindbladTohEtAl.because(stdpopsim.CiteReason.POP_SIZE)
],
)
stdpopsim.register_species(_species)
def test_add_duplicate_species(self):
species = stdpopsim.get_species("HomSap")
with self.assertRaises(ValueError):
stdpopsim.register_species(species)
import shutil
import string
import pathlib
import logging
import click
import black
import daiquiri
import stdpopsim
from . import ensembl
logger = logging.getLogger("maint")
species_template = string.Template(
"""
import stdpopsim
from . import genome_data
# [The following are notes for implementers and should be deleted
# once the recombination rates have been inserted]
# This is the per-chromosome recombination rate, typically the mean
# rate along the chromosome.
# Values in this dictionary are set to -1 by default, so you have
# to update each one. These should be derived from the most reliable
# data and how they were obtained should be documented here.
# The appropriate citation must be added to the list of
# recombination_rate_citations in the Genome object.
_recombination_rate = $chromosome_rate_dict
Command line interface for managing routine maintenance tasks.
This interface is for stdpopsim developers only.
"""
import contextlib
import shutil
import string
import pathlib
import click
import black
import stdpopsim
from . import ensembl
species_template = string.Template("""
import stdpopsim
from . import genome_data
_chromosomes = []
for name, data in genome_data.data["chromosomes"].items():
_chromosomes.append(
stdpopsim.Chromosome(
id=name,
length=data["length"],
synonyms=data["synonyms"],
mutation_rate=0, # FILL ME IN
recombination_rate=0, # FILL ME IN
)
)
