chrY 59373566 0.0
"""
_chromosomes = []
for line in _chromosome_data.splitlines():
name, length, mean_rr = line.split()[:3]
_chromosomes.append(
genomes.Chromosome(
name=name,
length=int(length),
default_mutation_rate=1e-8, # WRONG!,
default_recombination_rate=float(mean_rr)))
#: :class:`stdpopsim.Genome` definition for humans.
genome = genomes.Genome(species="homo_sapiens",
chromosomes=_chromosomes,
default_genetic_map=HapmapII_GRCh37.name)
#
# Experimental interface used to develop the CLI.
#
class TempChromosome(object):
"""
Temporary class while figuring out the best way to do this.
"""
def __init__(self):
self.length = None
self.recombination_map = None
self.mutation_rate = None
#
###########################################################
_chromosomes = []
_chromosomes.append(
genomes.Chromosome(name="chr",
length=4641652,
default_mutation_rate=1e-5 + 2e-4,
default_recombination_rate=0.0))
# mean_conversion_rate=8.9e-11 # not implemented yet!
# mean_conversion_length=542 # not implemented yet!
#: :class:`stdpopsim.Genome` definition for E. Coli.
# Chromosome length data is based on strain K-12.
genome = genomes.Genome(species="e_coli",
chromosomes=_chromosomes,
default_genetic_map=None)
###########################################################
#
# Demographic models
#
###########################################################
# TODO add a generation time here
# default_generation_time = -1
class LapierreConstant(models.Model):
"""
Model Name:
_chromosomes = []
for line in _chromosome_data.splitlines():
name, length = line.split()[:2]
_chromosomes.append(
genomes.Chromosome(
name=name,
length=int(length),
default_mutation_rate=8.4e-9, # WRONG!, underestimate used in S&S
default_recombination_rate=8.4e-9)
) # WRONG, underestimate used in S&S!
#: :class:`stdpopsim.Genome` definition for D. melanogaster. Chromosome length data is
#: based on `dm6 <https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4/>`_.
genome = genomes.Genome(species="drosophila_melanogaster",
chromosomes=_chromosomes,
default_genetic_map=Comeron2012_dm6.name)
###########################################################
#
# Demographic models
#
###########################################################
default_generation_time = 0.1
class SheehanSongThreeEpoch(models.Model):
"""
Model Name:
SheehanSongThreeEpoch
chr5 26975502
"""
# mutation rate from Ossowski 2010 Science
# recombination value from Huber et al 2014 MBE
# rho=200/Mb, assume Ne=124,000, rho=2*Ne*r
_chromosomes = []
for line in _chromosome_data.splitlines():
name, length = line.split()[:2]
_chromosomes.append(
genomes.Chromosome(name=name,
length=int(length),
default_mutation_rate=7e-9,
default_recombination_rate=8.1e-9))
genome = genomes.Genome(species="arabidopsis_thaliana",
chromosomes=_chromosomes,
default_genetic_map=Salome2012.name)
###########################################################
#
# Demographic models
#
###########################################################
class Durvasula2017MSMC(models.Model):
"""
Model estimated from two homozygous individuals from the South Middle Atlas
using MSMC
"""
def __init__(self):