def test_selfing_after_outcrossing(self):
"""Test scinario: generations of selfing after generations of outcrossing."""
# outcrossing
self.sim.evolve(initOps=self.initOps,
matingScheme=simu.RandomMating(
subPopSize=10,
sexMode=self.sexMode,
ops=[
simu.MendelianGenoTransmitter(),
cf.MyOutcrossingTagger()
]),
gen=10)
for pop in self.sim.populations():
for ind in pop.individuals():
assert ind.info('self_gen') == 0
assert pop.dvars().gen == 10
# selfing
self.sim.evolve(
initOps=self.initOps,
matingScheme=simu.SelfMating(
subPopSize=10,
sexMode=self.sexMode,
ops=[simu.SelfingGenoTransmitter(),
cf.MySelfingTagger()]),
gen=10)
for pop in self.sim.populations():
for ind in pop.individuals():
assert ind.info('self_gen') == 10
assert pop.dvars().gen == 20
def test_pure_selfing(self):
"""Test pure inbreeding population.
When all individuals undergo selfing, the values in `self_gen` should be identical
to the number of generations since simulations started.
"""
self.sim.evolve(
initOps=self.initOps,
matingScheme=simu.SelfMating(
subPopSize=10,
sexMode=self.sexMode,
ops=[simu.SelfingGenoTransmitter(),
cf.MySelfingTagger()]),
gen=10)
for pop in self.sim.populations():
for ind in pop.individuals():
assert ind.info('self_gen') == 10
# 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/>.
#
# 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 simuPOP as sim
pop = sim.Population(100, loci=5 * 3, infoFields='parent_idx')
pop.evolve(initOps=[sim.InitGenotype(freq=[0.2] * 5)],
preOps=sim.Dumper(structure=False, max=5),
matingScheme=sim.HomoMating(
sim.SequentialParentChooser(),
sim.OffspringGenerator(ops=[
sim.SelfingGenoTransmitter(),
sim.ParentsTagger(infoFields='parent_idx'),
])),
postOps=sim.Dumper(structure=False, max=5),
gen=1)
# 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 simuPOP as sim
def traj(gen):
return [0.5 + gen * 0.01]
pop = sim.Population(1000, loci=[10]*2)
# evolve the sim.Population while keeping allele frequency 0.5
pop.evolve(
initOps=[
sim.InitSex(),
sim.InitGenotype(freq=[0.5, 0.5])
],
matingScheme=sim.HomoMating(sim.RandomParentChooser(),
sim.ControlledOffspringGenerator(loci=5,
alleles=[0], freqFunc=traj,
ops = sim.SelfingGenoTransmitter())),
postOps=[
sim.Stat(alleleFreq=[5, 15]),
sim.PyEval(r'"%.2f\t%.2f\n" % (alleleFreq[5][0], alleleFreq[15][0])')
],
gen = 5
)
# 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 simuPOP as sim
pop = sim.Population(size=[1000],
loci=2,
infoFields=['father_idx', 'mother_idx'])
pop.setVirtualSplitter(sim.ProportionSplitter([0.2, 0.8]))
pop.evolve(
initOps=sim.InitSex(),
matingScheme=sim.HeteroMating(matingSchemes=[
sim.SelfMating(subPops=[(0, 0)],
ops=[sim.SelfingGenoTransmitter(),
sim.ParentsTagger()]),
sim.RandomMating(
subPops=[(0, 1)],
ops=[sim.SelfingGenoTransmitter(),
sim.ParentsTagger()])
]),
gen=10)
[int(ind.father_idx) for ind in pop.individuals(0)][:15]
[int(ind.mother_idx) for ind in pop.individuals(0)][:15]