def setup(parser):
config = parser.parse_args()
sim_id = uuid.uuid1().urn
script = __file__
if config.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
data.set_experiment_name(config.experiment)
data.set_database_hostname(config.dbhost)
data.set_database_port(config.dbport)
dbconfig = data.getMingConfiguration(data.modules)
ming.configure(**dbconfig)
# set up parallelism. At the moment, this doesn't do anything on OSX
# but should provide parallelism on Linux across the replicates at least
if config.cores is not None:
cores = config.cores
else:
cores = utils.get_parallel_cores(config.devel)
log.info("Setting up %s cores for parallel simulation", cores)
import simuOpt
if(config.debug == 1):
simuOpt.setOptions(alleleType='long',optimized=True,quiet=False,numThreads = cores)
else:
simuOpt.setOptions(alleleType='long',optimized=True,quiet=False,numThreads = cores)
return (config,sim_id,script, cores)
def rep_case_control(rep_opt,logger=None):
"""Given the gridding scheme options, create simuPOP files in the given subdirectories."""
simuOpt.setOptions(alleleType='binary', optimized=True)
from simuPOP import *
cc_opt = simuOpt.Params(singleGeneModel.options)
for maf in xrange(len(rep_opt.MAFs)):
for maf_rep in xrange(rep_opt.MAF_replicates):
maf_dir = "MAF_%.2f_%d" %(rep_opt.MAFs[maf],maf_rep+1)
cc_opt.expandPop = "%s/%s.pop" % (maf_dir,maf_dir)
cc_opt.pop = loadPopulation(cc_opt.expandPop)
logger.info("Expanded population %s loaded!" %cc_opt.expandPop)
for cc in xrange(len(rep_opt.CCs)):
for cc_rep in xrange(rep_opt.CC_replicates):
cc_dir = "cc_%d_%d" % (rep_opt.CCs[cc],cc_rep+1)
for wtr in xrange(len(rep_opt.WTRs)):
for wtr_rep in xrange(rep_opt.WTR_replicates):
wtr_dir = "WTR_%.2f_%d" % (rep_opt.WTRs[wtr],wtr_rep+1)
for grr in xrange(len(rep_opt.GRRs)):
for grr_rep in xrange(rep_opt.GRR_replicates):
grr_dir = "GRR_%.2f_%d" % (rep_opt.GRRs[grr],grr_rep+1)
dirpath = path_maker(maf_dir,cc_dir,wtr_dir,grr_dir)
cc_opt.wtr = rep_opt.WTRs[wtr]
cc_opt.GRR = rep_opt.GRRs[grr]
cc_opt.numControls= rep_opt.CCs[cc]
cc_opt.sampledPop = os.path.join(dirpath,"sample.pop")
pop = singleGeneModel.penetrance(cc_opt,logger)
case_control_dataset.save(pars.sampledPop)
logger.info("Sampled population saved at %s" %pars.sampledPop)
def setup(parser):
config = parser.parse_args()
sim_id = uuid.uuid1().urn
script = __file__
if config.debug == '1':
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
# set up parallelism. At the moment, this doesn't do anything on OSX
# but should provide parallelism on Linux across the replicates at least
if config.cores is not None:
cores = config.cores
else:
cores = int(utils.get_parallel_cores(config.devel))
log.info("Setting up %s cores for parallel simulation", cores)
import simuOpt
if (config.debug == 1):
simuOpt.setOptions(alleleType='long',
optimized=True,
quiet=False,
numThreads=cores)
else:
simuOpt.setOptions(alleleType='long',
optimized=True,
quiet=False,
numThreads=cores)
return (config, sim_id, script, cores)
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#!/usr/bin/env python
#
import simuOpt, os, sys, json
# use 'binary module' for representing long sequences
simuOpt.setOptions(optimized=True, alleleType="binary")
import simuPOP as sim
import random
from itertools import izip
from itertools import islice
from pprint import pprint
from bisect import bisect
from optparse import OptionParser
import my_timer
# equal fitness function
def eq_fit():
return 1
#!/usr/bin/env python # Copyright (c) 2013. Mark E. Madsen <*****@*****.**> # # This work is licensed under the terms of the Apache Software License, Version 2.0. See the file LICENSE for details. from __future__ import print_function import simuOpt, sys simuOpt.setOptions(alleleType='long',optimized=False,quiet=True) import simuPOP as sim import uuid import ctpy.data as data import ctpy.utils as utils import ctpy.math as cpm import ming import itertools import logging as log import argparse """ This program simulates the Wright-Fisher model of genetic drift with infinite-alleles mutation in a single population, and counts the number of alleles present in the population and in samples of specified size. This process is performed for each combination of key model parameters, and the results are saved to MongoDB. """ ## setup sargs = utils.ScriptArgs()
Simulation related code specific to mutational model (the infinite sites model).
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
# standard imports
import csv
import io
import sys
import simuOpt
simuOpt.setOptions(alleleType='binary')
import simuPOP as simu
from . import common as cf
from . import utils
def get_pure_hermaphrodite_mating(r_rate,
weight,
size,
loci,
allele_length,
field='self_gen'):
"""
Construct mating scheme for pure hermaphrodite with partial selfing under the
infinite sites model.
import simuPOP as sim import simuOpt simuOpt.setOptions(alleleType='short', quiet=True) import pandas as pd import numpy as np import collections np.set_printoptions(suppress=True, precision=3) from ggplot import * # create 3 subpops with different sizes pop = sim.Population(size=[3, 4, 5], ploidy=1, loci=1, infoFields='x') sim.dump(pop) # a diploid population pop = sim.Population(size=[10], ploidy=2, loci=10, infoFields='x') sim.dump(pop) # a tetraploid population pop = sim.Population(size=[10], ploidy=4, loci=10, infoFields='x') sim.dump(pop) # something with frequencies pop = sim.Population(10, ploidy=2, loci=[5]) sim.dump(pop) sim.initGenotype(pop, freq=[0.2, 0.3, 0.5]) sim.dump(pop) # access stuff pop = sim.Population(size=[2, 3],
"""Requires the simuPOP module be installed in the python path. Imports the results of a sampled population using the simuPOP methods.""" import simuOpt as inputsimuOpt inputsimuOpt.setOptions(quiet=True) import simuPOP as inputsimuPop def inRead(filename): """ Reads a binary file containing a population in simuPOP format. Returns the population as a simuPOP object. """ pop = inputsimuPop.loadPopulation(filename) return pop
#! /usr/bin/python
# This version comes from simu20-10GRACE.py
# It has larger population sizes and fewer loci
# Other population gentic variables are also recorded
import simuOpt
simuOpt.setOptions(numThreads=12, quiet=True, alleleType='long')
import simuPOP as sim
from simuPOP.utils import importPopulation, export
from simuPOP.sampling import drawRandomSample
#g = 5000 # gen
#u = 1e-6 # u
#m = 0 # m
#c = 400000 # contig
#r = 1.0/c # recomb
def SbPSz(gen):
if gen<50:
return [10]
if gen>999:
return [200]*10
else:
return [2000]
pop = sim.Population(size=[10], ploidy=2, loci=100000, chromNames=['Chr1'], # Find out whether simuPOP 'thinks' all these loci are on the same chromosome
alleleNames=['A', 'C', 'T', 'G'],
infoFields=['migrate_to'])
pop.evolve(
initOps=[
sim.InitSex(maleFreq=0.5),
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#
import simuOpt
simuOpt.setOptions(debug='DBG_WARNING')
import simuPOP as sim
pop = sim.Population(10, loci=3, chromNames=['chr1'])
# 1 1 1,
pop.setGenotype([1])
# 1 1 1, 0 0 0
pop.addChrom(lociPos=[0.5, 1, 2],
lociNames=['rs1', 'rs2', 'rs3'],
chromName='chr2')
pop1 = sim.Population(10,
loci=3,
chromNames=['chr3'],
lociNames=['rs4', 'rs5', 'rs6'])
# 2 2 2,
pop1.setGenotype([2])
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#!/usr/bin/env python
#
import simuOpt, os, sys, json
# use 'binary module' for representing long sequences
simuOpt.setOptions(optimized=True, alleleType='binary')
import simuPOP as sim
import random
from itertools import izip
from itertools import islice
from pprint import pprint
from bisect import bisect
from optparse import OptionParser
import my_timer
# equal fitness function
def eq_fit():
return 1
happens to the structure of trait trees, sampled at fixed intervals. We will leave in homophily, but ignore
convergence since it should be temporary with innovation_rateation/noise.
"""
import logging as log
from time import time
import argparse
import uuid
import seriationct.utils as utils
import simuOpt
simuOpt.setOptions(alleleType='long', optimized=True, quiet=False, numThreads=utils.get_parallel_cores(dev_flag=True))
import simuPOP as sim
import seriationct.demography as demo
global config, sim_id, script
def setup(parser):
config = parser.parse_args()
sim_id = uuid.uuid4().urn
script = __file__
if config.debug == '1':
# -*- mode: python; coding: utf-8; -*-
"""Import simuPOP's function and constant names."""
# import functions
import simuOpt
# we unconditionally use 'lineage' version of simuPOP as our interest is lineage.
simuOpt.setOptions(quiet = True,
alleleType = 'lineage')
from simuPOP import RandomMating, getRNG
import simuPOP
# import constants
from simuPOP import MALE, FEMALE, UNIFORM_DISTRIBUTION, \
AUTOSOME, CHROMOSOME_X, CHROMOSOME_Y, MITOCHONDRIAL, ALL_AVAIL, \
PER_LOCI, PER_INDIVIDUAL, PER_PLOIDY, PER_CHROMOSOME, \
BY_PROBABILITY, BY_PROPORTION, PROB_OF_MALES
# metadata of this package. This is likely to change once I start
# to use distutils2/packaging instead of setuptools/distutils.
# Then metadata is defined in PKG-INFO file.
from migselsim import metadata
def enum(*seq, **named):
enums = dict(zip(seq, range(len(seq))), **named)
return type('Enum', (), enums)
SCENARIO = enum('NOT_SPECIFIC', 'SEX_SPECIFIC', 'DEME_SPECIFIC', 'SEX_AND_DEME_SPECIFIC')
COMMAND = __name__.split('.')[0]
VERSION = metadata.__version__
#!/usr/bin/env python
import simuOpt, types
simuOpt.setOptions(alleleType='long', numThreads=2)
import simuPOP as sim
from simuPOP import *
from simuPOP.utils import *
from simuPOP.sampling import drawRandomSample
options = [
{
'name':'NA',
'default':5000,
'label':'Ancestral Population Size',
'type':[int, long],
'validator':simuOpt.valueGT(0),
'description':'Ancestral population size'
},
{
'name':'N1',
'default':1000,
'label':'Daugther 1 Population Size',
'type':[int, long],
'validator':simuOpt.valueGT(0),
'description':'Daughter 1 population size'
},
{
'name':'N2',
'default':1000,
'label':'Daugther 2 Population Size',
'type':[int, long],
'validator':simuOpt.valueGT(0),
'description':'Daughter 2 population size'
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#!/usr/bin/env python
#
import simuOpt, os, sys, time
# use 'mutant module' for representing long sequences
simuOpt.setOptions(optimized=True, alleleType='long')
import simuPOP as sim
import random
from itertools import izip
from pprint import pprint
from bisect import bisect
# equal fitness function
def eq_fit():
return 1
# modified version of model provided in User Guide (pg. 86-87)
def infSitesMutate(pop, param):
(startPos, endPos, rate) = param
#!/usr/bin/env python
#
# This example simulates recent and remote selective sweep and draw
# trio samples.
import sys, os, math, logging
import simuOpt
simuOpt.setOptions(alleleType='binary', optimized=False, gui=False)
from simuPOP import *
import loadHapMap3, selectMarkers, simuGWAS
def downloadData(chroms, logger):
'''
Download and create populations from the third phase of the HapMap3 data.
This equivalent to command
> loadHapMap3.py --chroms=2
'''
if not os.path.isdir('HapMap'):
os.mkdir('HapMap')
for chrom in chroms:
for popName in loadHapMap3.HapMap3_pops:
filename = 'HapMap/HapMap3_%s_chr%d.pop' % (popName, chrom)
if not os.path.isfile(filename):
pop = loadHapMap3.loadHapMapPop(chrom, popName, logger)
pop.save(filename)
def getInitPop(logger):
'''
import copy
import inspect
import math
import numpy as np
import networkx as nx
from matplotlib import pyplot as plt
from matplotlib.patches import Ellipse
from IPython.core.pylabtools import print_figure
from IPython.display import Image
import simuOpt
simuOpt.setOptions(gui=False, quiet=True)
import simuPOP as sp
from simuPOP import demography
def _hook_view(pop, param):
view = param
view.complete_cycle(pop)
return True
class Model:
def __init__(self, gens):
self._gens = gens
self._views = []
self.pop_size = 100
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#!/usr/bin/env python
#
import simuOpt, os, sys, json
# use 'mutant module' for representing long sequences
simuOpt.setOptions(optimized=True, alleleType='mutant')
import simuPOP as sim
import random
from itertools import izip
from itertools import islice
from pprint import pprint
from bisect import bisect
from optparse import OptionParser
import my_timer
# equal fitness function
def eq_fit():
return 1
#!/usr/bin/env python # # Purpose: # Testing penetrance. # # Author: # Bo Peng ([email protected]) # # $LastChangedRevision$ # $LastChangedDate$ # import unittest, os, sys from simuOpt import setOptions setOptions(quiet=True) new_argv = [] for arg in sys.argv: if arg in ['short', 'long', 'binary', 'mutant', 'lineage']: setOptions(alleleType=arg) elif arg.startswith('-j'): setOptions(numThreads=int(arg[2:])) else: new_argv.append(arg) sys.argv = new_argv from simuPOP import * class TestPenetrance(unittest.TestCase): def setUp(self): self.pop = Population(size=[500, 100, 1000], ploidy=2, loci=[1])
import simuOpt
simuOpt.setOptions(quiet=True, numThreads=4)
import simuPOP as sim
import os, numpy as np, pandas as pd, collections as col
from saegus import analyze, simulate, parameters
import pytest
@pytest.fixture(scope="session")
def tuson_pop():
tuson = sim.loadPopulation('tuson.pop')
return tuson
def test_info_fields(tuson_pop):
pop = tuson_pop
assert 'primary' in pop.infoFields(
), "Population lacks the primary infoField. Cannot assign structured mating."
},
#migration
{
'longarg': 'mig=',
'default': 0,
'label': 'migration model',
'allowedTypes': [types.IntType, types.LongType],
'description': '''0: No migration
|1: MigrIslandRates(r, n)
|2: MigrHierarchicalIslandRates([r11, r12], r2, [n1, n2])
|3: MigrSteppingStoneRates(r, n, circular=False)''',
'chooseOneOf': range(4),
'validate': simuOpt.valueOneOf(range(4))
}
]
simuOpt.setOptions(optimized=True, alleleType='long', quiet=True)
pars = simuOpt.simuParam(options, 'A demo simulation')
cfgPath = os.path.join(dirI, 'sample.cfg')
if os.path.exists(cfgPath):
pars.loadConfig(cfgPath)
if not pars.getParam():
sys.exit(1)
pars.saveConfig(os.path.join(dirI, 'sample.cfg'))
n_gen, n_pop, n_ind, n_loci, n_chrom, n_ploidy, n_allele, init_freq = \
pars.n_gen, pars.n_pop, pars.n_ind, pars.n_loci, pars.n_chrom, pars.n_ploidy, \
len(pars.allele), pars.init_freq
init_freq_2 = []
for freq in init_freq:
init_freq_2.append([freq, 1 - freq])
import simuOpt, os, sys, time, subprocess, errno, csv
simuOpt.setOptions(alleleType="lineage", quiet=True)
from simuPOP import *
from simuPOP.sampling import drawRandomSample
import datetime
from numpy import *
from itertools import *
homeDir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
options = [
{"name": "popSize", "default": 100, "label": "Population Size", "type": "integer", "validator": "popSize > 0"},
{"name": "sampSize", "default": 100, "label": "Sample Size", "type": "integer", "validator": "sampSize > 0"},
{"name": "loc", "default": 5, "label": "Number of Loci", "type": "integer", "validator": "loc > 0"},
{
"name": "allPerLoc",
"default": 10,
"label": "Number of Alleles per Loci",
"type": "integer",
"validator": "allPerLoc > 1",
},
{
"name": "generations",
"default": 50,
"label": "Number of Generations",
"type": "integer",
"validator": "generations >= 0",
},
{
"name": "replications",
#!/home/yairf/Develop/python/loopy/bin/python
import os, sys, re, math
import argparse
import numpy as np
import simuOpt
simuOpt.setOptions(quiet=True)
import simuPOP as sim
import math
from simuPOP.utils import *
#-----------------#
# Parse arguments #
#-----------------#
parser = argparse.ArgumentParser(
description=
"Backward simulation of selection using the simuPOP package. The input includes the demographic model, the current derived allele frequency, the selection coefficient, and the backward time window at which selection was active."
)
parser.add_argument("-g",
"--number_of_generations",
type=int,
default=10000,
help="The number of generations simulated \
(default = %(default)s).")
parser.add_argument(
dest="num_vars",
action='store_true',
help="print the number of variants post mut")
parser.add_argument("--len-trees",
"-l",
dest="len_trees",
action='store_true',
help="print the dist of tree lengths pre mut")
args = parser.parse_args()
if args.generations is None:
args.generations = args.popsize * args.multiplier
from simuOpt import setOptions
setOptions(alleleType='mutant')
setOptions(optimized=True)
if not args.verbose:
setOptions(quiet=True)
import simuPOP as sim
sim.setRNG(seed=args.seed)
random.seed(args.seed)
logfile = fileopt(args.logfile, "w")
logfile.write("Options:\n")
logfile.write(str(args) + "\n")
logfile.write(time.strftime('%X %x %Z') + "\n")
logfile.write("----------\n")
'''
This python module provides several utility functions that handles HapMap
populations. When used as a script, this module creates a population using
selected markers and populations.
'''
import simuOpt as opt
opt.setOptions(alleleType='lineage', quiet=True, optimized=True)
from simuPOP import *
from types import *
import os
import sys
import random
import string
def mergeHapMapPops(HapMap_dir, HapMap_pops, chrom, logger=None):
'''
Load HapMap dataset for multiple populations and merge them.
The important step is to find a common set of markers and make sure
alleles are recoded if necessary. (Alleles are sometimes coded differently
in different HapMap populations.)
HapMap_dir
Directory where HapMap files (in simuPOP format) are saved.
HapMap_pops
HapMap populations to load.
chrom
import simuOpt
simuOpt.setOptions(alleleType='lineage', optimized=True, quiet=True)
import simuPOP as sim
import pandas as pd
import collections as col
from wgs import breed, operators, selection, helpers, parser, parameterizer, selection
import random
import numpy as np
np.set_printoptions(suppress=True, precision=3)
import matplotlib.pyplot as plt
hapmap = pd.read_csv('clean_hapmap.txt')
genetic_map = hapmap.ix[:, :'cM_pos']
genetic_map = pd.read_csv('nam_prefounders_genetic_map.txt',
index_col=None,
sep='\t')
chr_cm_positions = col.OrderedDict()
for i in range(1, 11):
chr_cm_positions[i] = []
for idx in range(len(genetic_map)):
chr_cm_positions[int(genetic_map.iloc[idx]['chr'])].append(
float(genetic_map.iloc[idx]['cM_pos']))
cM_positions = []
for k, v in chr_cm_positions.items():
cM_positions.append(v)
snp_to_integer = {'A': 0, 'C': 1, 'G': 2, 'T': 3, '-': 4, '+': 5}
# Software is furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice (including the next
# paragraph) shall be included in all copies or substantial portions of the
# Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
import simuOpt
simuOpt.setOptions(quiet=True, alleleType='binary')
import simuPOP as simu
import partial_selfing.common as cf
import partial_selfing.infinite_sites as isf
class TestRecordSelfing:
def setUp(self):
# A locus with 10 sites
"Let there are 5 loci with 2 sites each"
self.allele_length = 2
self.loci = 5
self.pop = simu.Population(size=10,
loci=self.allele_length * self.loci,
infoFields='self_gen')
selfingsim.infinite_alleles
===========================
Simulation related code specific to mutational model (the infinite alleles model).
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import csv
import io
import sys
import simuOpt
simuOpt.setOptions(alleleType='long')
import simuPOP as simu
from . import common as cf
from . import utils
def get_init_genotype_by_prop(prop):
"""
Sets up initial genotypes of initial individuals by specifying frequencies of
alleles.
"""
s = sum(prop)
return (len(prop), simu.InitGenotype(prop=[p / s for p in prop]))
def get_mutation_operator(m_rate, loci, nrep, burnin, new_idx=0):
selfingsim.infinite_alleles
===========================
Simulation related code specific to mutational model (the infinite alleles model).
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import csv
import io
import sys
import simuOpt
simuOpt.setOptions(alleleType='long')
import simuPOP as simu
from . import common as cf
from . import utils
def get_init_genotype_by_prop(prop):
"""
Sets up initial genotypes of initial individuals by specifying frequencies of
alleles.
"""
s = sum(prop)
return (len(prop), simu.InitGenotype(prop=[p / s for p in prop]))
def get_mutation_operator(m_rate, loci, nrep, burnin, new_idx=0):
"""
import simuOpt
simuOpt.setOptions(alleleType='short', optimized=True, quiet=True)
import simuPOP as sim
import pandas as pd
import collections as col
from wgs import breed, operators, selection, helpers, parser, parameterizer, selection
import random
import numpy as np
np.set_printoptions(suppress=True, precision=3)
import matplotlib.pyplot as plt
hapmap = pd.read_csv('clean_hapmap.txt')
genetic_map = hapmap.ix[:, :'cM_pos']
genetic_map = pd.read_csv('nam_prefounders_genetic_map.txt',
index_col=None,
sep='\t')
chr_cm_positions = col.OrderedDict()
for i in range(1, 11):
chr_cm_positions[i] = []
for idx in range(len(genetic_map)):
chr_cm_positions[int(genetic_map.iloc[idx]['chr'])].append(
float(genetic_map.iloc[idx]['cM_pos']))
cM_positions = []
for k, v in chr_cm_positions.items():
cM_positions.append(v)
snp_to_integer = {'A': 0, 'C': 1, 'G': 2, 'T': 3, '-': 4, '+': 5}
#Python 2.7.5 (default, May 15 2013, 22:43:36) [MSC v.1500 32 bit (Intel)] on win32
#Type "copyright", "credits" or "license()" for more information.
from simuOpt import setOptions
setOptions(quiet=True)
import simuPOP as sim
from simuPOP.utils import importPopulation
pop = importPopulation('GENEPOP', 'Genpop_2subpops.txt')
import random
pop.addInfoFields(['age'])
# age_cat is not imported as they are defined by age
# 0, 1, 2 as juvenile and 2-above as adult
with open('Fstat_dat(age,agecat,sex).txt') as fs:
for idx, line in enumerate(fs):
if idx < 10:
# skip the first few lines
continue
if line.startswith('1 '):
age, age_cat, sex = line.strip().split()[-3:]
pop.individual(idx -
18).setSex(sim.MALE if sex == '2' else sim.FEMALE)
pop.individual(idx - 18).age = int(age)
#pop.individual(idx-18).age_cat = int(age_cat)
elif line.startswith('2 '):
age_cat, sex = line.strip().split()[-2:]
pop.individual(idx -
18).setSex(sim.MALE if sex == '2' else sim.FEMALE)
# no age info
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#
import simuOpt
simuOpt.setOptions(alleleType='lineage', quiet=True)
import simuPOP as sim
pop = sim.Population(1000, loci=[10]*4)
pop.evolve(
initOps=[
sim.InitSex(),
sim.InitGenotype(freq=[0.25]*4),
sim.InitLineage(range(1000), mode=sim.PER_INDIVIDUAL),
],
matingScheme=sim.RandomMating(ops=sim.Recombinator(rates=0.001)),
gen = 100
)
# average number of 'contributors'
num_contributors = [len(set(ind.lineage())) for ind in pop.individuals()]
print('Average number of contributors is %.2f' % (sum(num_contributors) / float(pop.popSize())))
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import simuOpt
simuOpt.setOptions(
quiet = True,
alleleType = 'long')
import genealogy as genea
genealogy = [genea.Genealogy(24)]
class Reindexer(sim.PyOperator):
def __init__(self, loci, *args, **kwargs):
self._loci = loci
sim.PyOperator.__init__(self, func = self.reindex, *args, **kwargs)
def reindex(self, pop):
loci = self._loci
marker = loci[0]
#! /usr/bin/python # The A.1A simuPOp example # Use simuOpt to import options import simuOpt simuOpt.setOptions(quiet=True, numThreads=4, gui=True) #This simuOpt allows selection of one of the six simuPOP modules #setOptions(optimized=False, alleleType='long', quiet=True) import simuPOP as sim # Set up th epopulation, ploidy is 2 by default, add (1000)*5 to make # 5 populations pop = sim.Population(size=1000, loci=2) pop.evolve( initOps=[ # Initialize individuals with random sex (MALE or FEMALE) sim.InitSex(), # Initialize individuals with two haplotypes. sim.InitGenotype(haplotypes=[[1, 2], [2, 1]]) ], # Random mating using a recombination operator matingScheme=sim.RandomMating(ops=sim.Recombinator(rates=0.01)), postOps=[ # Calculate Linkage Disequilibrium between two loci sim.Stat(LD=[0, 1], step=10), # Print calculated LD values sim.PyEval(r"'%2d: %.2f\n' % (gen, LD[0][1])", step=10), ], gen=100 )
import fileio
experiment = fileio.Experiment( constant_pop_size = 200, # Nance and Kearsey: 200k
a = 0.01304, # Nance and Kearsey: 0.01304
aa_fitness = 1.5, # Nance and Kearsey: 1.0
aa_homogamy = 0.9, # Nance and Kearsey: 0.9
deafness_freq = 0.0008, # Nance and Kearsey: look again
generations = 20, # Nance and Kearsey: 5 gen with 0 fitness + 20 gen with 1.0 fitness
simulations = 5000) # Nance and Kearsey: unspecified
import os
import time
import random
import argparse
import subprocess
import multiprocessing
import simuOpt
simuOpt.setOptions(optimized=True, numThreads=0, quiet=True)
import simuPOP as sim
def customChooser(pop, subPop):
'''
Generator function which chooses parents.
Upon initialization, this chooser mates couples in a monogamous
mating scheme.
The algorithm goes through each eligible person listwise.
If that person is deaf, that person marries deaf or not based on the
probability set by aa_homogamy. Further, if either
parent is deaf, their number of offspring is based on the
fitness set by aa_fitness (non-integer fitnesses are handled using a
randomizer for the fractional amount).
# required).
#
# Change Log:
# 2009-06-25 Bo Peng <*****@*****.**>
#
# Add functions mergeHapMapPops and getHapMapMarkers
#
'''
This python module provides several utility functions that handles HapMap
populations. When used as a script, this module creates a population using
selected markers and populations.
'''
import simuOpt
simuOpt.setOptions(alleleType='binary', quiet=True, version='1.0.1')
from simuPOP import *
from types import *
import os, sys, exceptions
def mergeHapMapPops(HapMap_dir, HapMap_pops, chrom, logger=None):
'''
Load HapMap dataset for multiple populations and merge them.
The important step is to find a common set of markers and make sure
alleles are recoded if necessary. (Alleles are sometimes coded differently
in different HapMap populations.)
HapMap_dir
Directory where HapMap files (in simuPOP format) are saved.
parser.add_option("-w","--width",dest="width",help="width of square grid, in populations",default=3)
parser.add_option("-L","--length",dest="length",help="number of bp in the chromosome",default=1e4)
parser.add_option("-l","--nloci",dest="nloci",help="number of selected loci",default=20)
parser.add_option("-m","--migr",dest="migr",help="migration proportion between adjacent populations",default=.01)
parser.add_option("-u","--mut_rate",dest="mut_rate",help="mutation rate of selected alleles",default=1e-7)
parser.add_option("-r","--recomb_rate",dest="recomb_rate",help="recombination rate",default=2.5e-8)
parser.add_option("-a","--gamma_alpha",dest="gamma_alpha",help="alpha parameter in gamma distributed selection coefficients",default=.23)
parser.add_option("-b","--gamma_beta",dest="gamma_beta",help="beta parameter in gamma distributed selection coefficients",default=5.34)
parser.add_option("-o","--outfile",dest="outfile",help="name of output file (or '-' for stdout)",default="-")
parser.add_option("-g","--logfile",dest="logfile",help="name of log file (or '-' for stdout)",default="-")
parser.add_option("-s","--selloci_file",dest="selloci_file",help="name of file to output selected locus information",default="sel_loci.txt")
parser.add_option("-t","--num_threads",dest="num_threads",help="Number of threads (MORE THREADS=SLOWER?!?!).",default=1)
(options,args) = parser.parse_args()
import simuOpt
simuOpt.setOptions(alleleType='mutant')
simuOpt.setOptions(numThreads = int(options.num_threads))
import simuPOP as sim
from simuPOP.demography import migr2DSteppingStoneRates
outfile = fileopt(options.outfile, "w")
logfile = fileopt(options.logfile, "w")
selloci_file = options.selloci_file
logfile.write("Options:\n")
logfile.write(str(options)+"\n")
generations=int(options.generations)
popsize=int(options.popsize)
nloci=int(options.nloci)
width=int(options.width)
#
# random fitness effect
#
from simuOpt import setOptions
setOptions(alleleType='mutant', quiet=True)
import simuPOP as sim
class RandomFitness:
def __init__(self, scale=1):
self.coefMap = {}
self.scale = scale
def _newS(self, loc, alleles):
raise ValueError(
"This function should be redefined in the subclass of this class")
def __call__(self, loc, alleles):
# because s is assigned for each locus, we need to make sure the
# same s is used for fitness of genotypes 01 (1-s) and 11 (1-2s)
# at each locus
if loc in self.coefMap:
s, h = self.coefMap[loc]
else:
res = self._newS(loc, alleles)
if type(res) in [list, tuple]:
if len(res) != 2:
raise ValueError("A list or tuple of s, h is expected")
s, h = res
else:
s = res
import simuOpt
# I use the lineage module to keep track of allele lineages.
simuOpt.setOptions(alleleType = 'lineage')
from simuPOP.utils import viewVars
from simuPOP import *
# This class is to recombine only in females. Note that it comes from an example
# in the simuPOP manual (sexSpecificRecombinator.py), but Bo Peng had to correct
# it after I told him it didn't work. The default loci and maleLoci were not well
# defined.
class sexSpecificRecombinator(PyOperator):
def __init__(self, intensity=0, rates=0, loci=ALL_AVAIL, convMode=NO_CONVERSION,
maleIntensity=0, maleRates=0, maleLoci=ALL_AVAIL, maleConvMode=NO_CONVERSION,
*args, **kwargs):
# This operator is used to recombine maternal chromosomes
self.Recombinator = Recombinator(rates, intensity, loci, convMode)
# This operator is used to recombine paternal chromosomes
self.maleRecombinator = Recombinator(maleRates, maleIntensity,
maleLoci, maleConvMode)
#
PyOperator.__init__(self, func=self.transmitGenotype, *args, **kwargs)
#
def transmitGenotype(self, pop, off, dad, mom):
# Form the first homologous copy of offspring.
self.Recombinator.transmitGenotype(mom, off, 0)
# Form the second homologous copy of offspring.
self.maleRecombinator.transmitGenotype(dad, off, 1)
return True
#pop = Population(2, loci=1000, infoFields=['ind_id', 'father_idx', 'mother_idx'])
#!/usr/bin/env python
#
# This example simulates a case-control sample using a GxE model.
#
import sys, os, random, math, logging
import simuOpt
simuOpt.setOptions(gui=False, alleleType='binary', optimized=True)
from simuPOP import *
import loadHapMap3, selectMarkers, simuGWAS
def downloadData(chroms, logger):
'''
Download and create populations from the third phase of the HapMap3 data.
This equivalent to command
> loadHapMap3.py --chroms='[2, 5,10]' --dest=HapMap
'''
if not os.path.isdir('HapMap'):
os.mkdir('HapMap')
for chrom in chroms:
for popName in loadHapMap3.HapMap3_pops:
filename = 'HapMap/HapMap3_%s_chr%d.pop' % (popName, chrom)
if not os.path.isfile(filename):
pop = loadHapMap3.loadHapMapPop(chrom, popName, logger)
pop.save(filename)
def getInitPop(logger):
#! /usr/bin/python #Object: Hierarchically structured Isolation with Migration model #Aim: Simulating SNPs data for genom scan methods comparison #Author: Pierre de Villemereuil #October 2013 #************************************************************************************ #---------------------------------Header--------------------------------------------- #************************************************************************************ #Setting allele size from simuOpt import setOptions setOptions(alleleType='binary') #Binary for two alleles states (SNPs) #Importing simuPOP import simuPOP as sim from simuPOP.utils import saveCSV from simuPOP.sampling import drawRandomSample #Importing some other python libraries from math import * from numpy import * from random import * #********************************************************************************************** #-----------------------------Simulation parameters------------------------------------------- #********************************************************************************************** #Population(s) size(s) popsize = 500
import simuOpt
simuOpt.setOptions(quiet=True, alleleType='binary')
import simuPOP as sim
pop = sim.Population(size=[10000] * 3, loci=[1] * 2, infoFields='fitness')
simu = sim.Simulator(pop, rep=3)
simu.evolve(initOps=[sim.InitSex(),
sim.InitGenotype(freq=[0.5, 0.5])],
preOps=[
sim.MaSelector(loci=0, fitness=[1, 0.99, 0.98], reps=0),
sim.MaSelector(loci=0, fitness=[1, 1, 0.99], reps=1),
sim.MlSelector([
sim.MaSelector(loci=0, fitness=[1, 0.99, 0.98]),
sim.MaSelector(loci=1, fitness=[1, 1, 0.99])
],
mode=sim.MULTIPLICATIVE,
reps=2)
],
matingScheme=sim.RandomMating(),
postOps=[
sim.Stat(alleleFreq=[0, 1], step=50),
sim.PyEval(r"'%.3f\t' % alleleFreq[0][1]", reps=0, step=50),
sim.PyEval(r"'%.3f\t' % alleleFreq[0][1]", reps=1, step=50),
sim.PyEval(
r"'%.3f\t%.3f\n' % (alleleFreq[0][1], alleleFreq[1][1])",
reps=2,
step=50),
],
gen=151)
#!/usr/bin/env python
# Copyright (c) 2013. Mark E. Madsen <*****@*****.**>
#
# This work is licensed under the terms of the Apache Software License, Version 2.0. See the file LICENSE for details.
from __future__ import print_function
import simuOpt, sys
simuOpt.setOptions(alleleType='long', optimized=False, quiet=True)
import simuPOP as sim
import uuid
import rapanuisim.data as data
import rapanuisim.utils as utils
import rapanuisim.math as cpm
import ming
import logging as log
import pprint as pp
import argparse
"""
This program simulates the Wright-Fisher model of genetic drift with infinite-alleles mutation in a single
population, and counts the number of alleles present in the population and in samples of specified size
"""
# get all parameters
args = argparse.ArgumentParser()
args.add_argument("--popsize", default=1000, type=int, help="Population Size")
args.add_argument("--stepsize",
default=100,
type=int,
help="Interval Between Data Samples")
args.add_argument(
"--length",
a_FREQ = 0.01304 # Nance and Kearsey: 0.01304
aa_FITNESS = 1.0 # Nance and Kearsey: 1.0
aa_HOMOGAMY = 0.9 # Nance and Kearsey: 0.9
DEAF_FREQ = 0.0008 # Nance and Kearsey: two other genes each at 0.003^2 freq (tiny)
GENERATIONS = 20 # Nance and Kearsey: 5 gen with 0 fitness + 20 gen with 1.0 fitness
SIMULATIONS = 5000
import os
import time
import random
import argparse
import subprocess
import multiprocessing
import simuOpt
simuOpt.setOptions(optimized=True, numThreads=0, quiet=True)
import simuPOP as sim
import fileio
def customChooser(pop, subPop):
'''
Generator function which chooses parents.
Upon initialization, this chooser mates couples in a monogamous
mating scheme.
The algorithm goes through each eligible person listwise.
If that person is deaf, that person marries deaf or hearing based on the
probability set by aa_homogamy. Further, if either
parent is deaf, their number of offspring is based on the
#==================================================================================================================== ###################################### Contact : [email protected] ##################################### #==================================================================================================================== #====================== Path ======================# PATHF = os.path.join( '/home/clement/Documents/SimulationPP') #BEWARE : insert your path line 65 #====================== Packages ======================# import math, os, time, random, sys, subprocess, shutil import simuPOP as sim import simuOpt from simuOpt import setOptions setOptions(optimized=False, alleleType='short', numThreads=2, quiet=True) import simuPOP.utils as utils from simuPOP.utils import saveCSV, export #====================== Variables ======================# nb_indiv = int(sys.argv[1]) #Number of individuals in the total population nb_loci = int(sys.argv[2]) #Number of locii nb_gen = int(sys.argv[3]) #Number of studied generations selection_intensity_z1 = int(sys.argv[4]) #Intensity of the selection repeat = int(sys.argv[5])
# Change Log:
# 2012-05-20 Matt Johnson <*****@*****.**>
# Modify to use in DPLSim
# 2010-03-01 Bo Peng <*****@*****.**>
# Add script.
'''
This script evolves a population forward in time, subject to rapid population
expansion, mutation, recombination and natural selection. A trajectory simulation
method is used to control the allele frequency of optional disease predisposing
loci. A scaling approach can be used to improve efficiency when weak, additive
genetic factors are used.
'''
import simuOpt
simuOpt.setOptions(alleleType='binary', version='1.0.1', optimized=False, quiet=True)
from simuPOP import *
from simuPOP.utils import simulateForwardTrajectory, simulateBackwardTrajectory, migrSteppingStoneRates
import os, sys, math, types, time
options = [
{'longarg': 'initPop=',
'default': 'init.pop',
'label': 'Initial population',
'allowedTypes': types.StringType,
'validate': simuOpt.valueValidFile(),
'description': 'An initial population created using script selectedMarkers.py'
},
{'longarg': 'dumpRec=',
# # Identical QTL Parameters
#
# ### Twenty Loci
#
# This simulates 20 replicates of recurrent selection.
# Each replicate has the same QTL and allele effects.
#
# ### Generating Data for GWAS with TASSEL
# In[ ]:
import simuOpt
simuOpt.setOptions(alleleType='short',
optimized=True,
numThreads=4,
quiet=True)
import simuPOP as sim
import pandas as pd
import collections as col
from saegus import breed, operators, simulate, analyze, parse, parameters
import random
import copy
import yaml
import numpy as np
np.set_printoptions(suppress=True, precision=3)
# In[ ]:
hapmap = pd.read_csv('clean_hapmap.txt')
from __future__ import division
from collections import defaultdict, OrderedDict
from copy import deepcopy
import psutil
import simuOpt
simuOpt.setOptions(alleleType='long', optimized=True, quiet=False)
simuOpt.setOptions(numThreads=psutil.cpu_count())
import math
import seaborn as sns
sns.set_style('white')
import matplotlib.pyplot as plt
import networkdrift.demography.network as network
from networkdrift.utils import utils
import simuPOP as sp
import logging as log
import numpy as np
import scipy.stats
import argparse
import uuid
from time import time
import sys
import os
from collections import defaultdict
import csv
global config, sim_id, script, cores
'''
Example use of script.
parameter-sweep-for-localization.py
--experiment paramsweep5 --networkfile smallworld --numloci 1 --maxinittraits 100
import simuOpt
simuOpt.setOptions(gui=False, alleleType='binary')
import simuPOP as sim
import random, math
from ch6_genCaseCtrl import genCaseControlSample
def penetrance(alpha, beta1, beta2, beta3, gamma1, gamma2):
def func(geno):
e = random.randint(0, 1)
g1 = geno[0] + geno[1]
g2 = geno[2] + geno[3]
logit = alpha + beta1 * g1 + beta2 * g2 + beta3 * g1 * g2 + gamma1 * e * g1 + gamma2 * e * g2
return 1 / (1. + math.exp(-logit))
return func
sample = genCaseControlSample(
pop, 1000, 1000,
sim.PyPenetrance(func=penetrance(-5, 0.20, 0.4, 0.4, 0.2, 0.4),
loci=['rs4491689', 'rs6869003']))
sim.stat(sample, association=sim.ALL_AVAIL)
# get p-values
sample.dvars().Allele_ChiSq_p
""" Functions for removing SNPs from simuPOP population objects. removeRare: removes SNPs with minor allele frequencies below a threshold. The threshold defaults are 0.0000001 or 0.999999, meaning only monomorphic loci are removed. A list of names of Disease Loci are required. writeSNPLoc: writes a text file with the name of each DPL and the new index location. This function is useful for the programs which do not use marker names or locations, to later identify the causative SNP. removeDPL: removes the DPL """ import simuOpt simuOpt.setOptions(alleleType='binary', optimized=True,quiet=True) import simuPOP as sim def removeRare(pop,thresh_hi=0.999999,thresh_lo=0.000001,DPL=['rs4491689'],savefile=False): """ Removes rare SNPs with a minor allele frequency below a threshold value. The default thresholds will only remove monomorphic loci. If savefile=False, the population is simply modified. Set savefile to a string to save the population to a binary file. The function returns: the number of loci removed a list of the the relative locations of the DPL. """ sim.stat(pop,alleleFreq=range(pop.totNumLoci())) lociToRemove = [l for l in xrange(pop.totNumLoci()) if pop.dvars().alleleFreq[l][0] > thresh_hi or pop.dvars().alleleFreq[l][0] < thresh_lo] pop.removeLoci(lociToRemove) if savefile:
elif alleleType == 'binary':
size = (memsize * 1024.0 * 1024.0 * 1024.0) / (
(loci * ploidy / 8.0 + 32.0) * 2.0 + 8)
mating = timeit.Timer(
setup='from __main__ import Population, InitSex, RandomMating,'
'MendelianGenoTransmitter\n'
"pop = Population(size=%d, loci=%d, ploidy = %d)" %
(size, loci, ploidy),
stmt="pop.evolve(\n"
"initOps=InitSex(),\n"
"matingScheme=RandomMating(ops=MendelianGenoTransmitter()),\n"
"gen=%d)" % gen)
print(">Maximum number of population size: %d\n>Time(sec):%f" %
(size, mating.timeit(number=1)))
if __name__ == '__main__':
# Number of processors(CPU Core)
numThreads = 1
alleleType = 'mutant'
from simuOpt import setOptions
setOptions(quiet=True)
setOptions(alleleType=alleleType)
setOptions(numThreads=numThreads)
from simuPOP import *
print("How many individuals can we simulate in 8GB of ram for")
for N, theta in [(1000, 1000), (1000, 5000), (1000, 10000), (5000, 1000),
(5000, 5000)]:
print("T =", 10 * N, " generations; theta =", theta, "?")
memory(N, theta)
parser.add_argument("--recomb_rate","-r", type=float, help="recombination rate",default=2.5e-8)
parser.add_argument("--selection_coef","-S", type=float, help="strength of selection",default=.1)
parser.add_argument("--nsamples","-k", type=int, help="number of *diploid* samples, total")
parser.add_argument("--ancestor_age","-A", type=int, help="time to ancestor above beginning of sim")
parser.add_argument("--mut_rate","-U", type=float, help="mutation rate",default=1e-7)
parser.add_argument("--treefile","-t", type=str, help="name of output file for trees (default: not output)")
parser.add_argument("--outfile","-o", type=str, help="name of output VCF file (default: not output)")
parser.add_argument("--logfile","-g", type=str, help="name of log file (or '-' for stdout)",default="-")
parser.add_argument("--selloci_file","-s", type=str, help="name of file to output selected locus information")
parser.add_argument("--samples_file", "-e", help="name of file to output information on samples (default=(dir)/samples.tsv)")
args = parser.parse_args()
import simuOpt
simuOpt.setOptions(alleleType='mutant')
import simuPOP as sim
if args.selloci_file is None:
args.selloci_file = os.path.join(os.path.dirname(args.treefile),"sel_loci.txt")
if args.samples_file is None:
args.samples_file = os.path.join(os.path.dirname(args.treefile),"samples.tsv")
samples_file = fileopt(args.samples_file,"w")
if args.outfile is not None:
outfile = fileopt(args.outfile, "w")
logfile = fileopt(args.logfile, "w")
logfile.write("Options:\n")
logfile.write(str(args)+"\n")
logfile.write(time.strftime('%X %x %Z')+"\n")
import simuOpt
simuOpt.setOptions(quiet=True, alleleType='long')
import simuPOP as sim
pop = sim.Population(size=[2500]*10, loci=1)
simu = sim.Simulator(pop, rep=2)
simu.evolve(
initOps=[
sim.InitSex(),
sim.InitGenotype(genotype=20),
],
preOps=[
sim.StepwiseMutator(rates=0.0001, reps=0),
sim.KAlleleMutator(k=10000, rates=0.0001, reps=1),
],
matingScheme=sim.RandomMating(),
postOps=[
# Use vars=['alleleFreq_sp'] to calculate allele frequency for
# each subpopulation
sim.Stat(alleleFreq=0, vars=['alleleFreq_sp'], step=200),
sim.PyEval('gen', step=200, reps=0),
sim.PyEval(r"'\t%.2f' % (sum([len(subPop[x]['alleleFreq'][0]) "
"for x in range(10)])/10.)", step=200),
sim.PyOutput('\n', reps=-1, step=200)
],
gen=601
)
=========================
Simulation related code specific to mutational model (the infinite sites model).
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
# standard imports
import csv
import io
import sys
import simuOpt
simuOpt.setOptions(alleleType='binary')
import simuPOP as simu
from . import common as cf
from . import utils
def get_pure_hermaphrodite_mating(r_rate, weight, size, loci, allele_length, field='self_gen'):
"""
Construct mating scheme for pure hermaphrodite with partial selfing under the
infinite sites model.
A fraction, 0 <= weight <= 1, of offspring is generated by selfing, and others are
generated by outcrossing. In this model, there is no specific sex so that any
individual can mate with any other individuals in a population.
Furthermore, a parent can participate in both selfing and outcrossing.
