def testSingleLocusChromosomeX(self):
sel = MySelectorProvider(self.pop, [1], [0], [self.fs], [self.ms])
selectors = sel.setSelector()
for s in selectors:
s.apply(self.pop)
for i in range(2):
if i == 0:
f = [1.0, self.fs, self.fs**2]
m = [1.0, self.ms]
else:
f = [self.fs**2, self.fs, 1.0]
m = [self.ms, 1.0]
for ind in self.pop.individuals(subPop=[i]):
if ind.sex() == sim.FEMALE:
genotype = tuple(ind.allele(0, ploidy=p, chrom=1)
for p in range(2))
if genotype == (0, 0):
self.assertAlmostEqual(ind.fitness, f[0])
elif genotype == (0, 1) or genotype == (1, 0):
self.assertAlmostEqual(ind.fitness, f[1])
else:
self.assertAlmostEqual(ind.fitness, f[2])
else:
genotype = tuple(ind.allele(0, ploidy=0, chrom=1)
for p in range(1))
if genotype == (0,):
self.assertAlmostEqual(ind.fitness, m[0])
else:
self.assertAlmostEqual(ind.fitness, m[1])
def testSingleLocusMitochondria(self):
sel = MySelectorProvider(self.pop, [3], [0], [self.fs], [self.ms])
selectors = sel.setSelector()
for s in selectors:
s.apply(self.pop)
for i in range(2):
if i == 0:
f = [1.0, self.fs]
m = [1.0, self.ms]
else:
f = [self.fs, 1.0]
m = [self.ms, 1.0]
for ind in self.pop.individuals(subPop=[i]):
genotype = tuple(ind.allele(0, ploidy=p, chrom=3)
for p in range(2))
if ind.sex() == sim.FEMALE:
if genotype == (0, 0):
self.assertAlmostEqual(ind.fitness, f[0])
else:
self.assertAlmostEqual(ind.fitness, f[1])
if ind.sex() == sim.MALE:
if genotype == (0, 0):
self.assertAlmostEqual(ind.fitness, m[0])
else:
self.assertAlmostEqual(ind.fitness, m[1])
def testTwoLociYMt(self):
sel = MySelectorProvider(self.pop,
[2, 3], [0, 0],
[self.fs, self.fs],
[self.ms, self.ms])
selectors = sel.setSelector()
for s in selectors:
s.apply(self.pop)
for i in range(2):
if i == 0:
# # of "1" alleles
f = [1.0, self.fs]
m = [1.0, self.ms, self.ms**2]
else:
f = [self.fs, 1.0]
m = [self.ms**2, self.ms, 1.0]
for ind in self.pop.individuals(subPop=[i]):
# Mitochondria
genotype = len([1 for i in
ind.genotype(chroms = [3],
ploidy = 0)
if i == 1])
if ind.sex() == sim.FEMALE:
self.assertAlmostEqual(ind.fitness, f[genotype])
else:
# Chromosome Y
genotype += len([1 for i in
ind.genotype(chroms = [2],
ploidy = 1)
if i == 1])
self.assertAlmostEqual(ind.fitness, m[genotype])
def testSingleLocusChromosomeY(self):
sel = MySelectorProvider(self.pop, [2], [0], [self.fs], [self.ms])
selectors = sel.setSelector()
for s in selectors:
s.apply(self.pop)
for i in range(2):
if i == 0:
m = [1.0, self.ms]
else:
m = [self.ms, 1.0]
for ind in self.pop.individuals(subPop=[i]):
if ind.sex() == sim.MALE:
genotype = tuple(ind.allele(0, ploidy=1, chrom=2)
for p in range(1))
if genotype == (0,):
self.assertAlmostEqual(ind.fitness, m[0])
else:
self.assertAlmostEqual(ind.fitness, m[1])
def testThreeLociAXY(self):
sel = MySelectorProvider(self.pop,
[0, 1, 2], [0, 0, 0],
[self.fs, self.fs, self.fs],
[self.ms, self.ms, self.ms])
selectors = sel.setSelector()
for s in selectors:
s.apply(self.pop)
for i in range(2):
if i == 0:
# # of "1" alleles
f = [1.0, self.fs, self.fs**2, self.fs**3, self.fs**4]
m = [1.0, self.ms, self.ms**2, self.ms**3, self.ms**4]
else:
f = [self.fs**4, self.fs**3, self.fs**2, self.fs, 1.0]
m = [self.ms**4, self.ms**3, self.ms**2, self.ms, 1.0]
for ind in self.pop.individuals(subPop=[i]):
# Autosome
genotype = len([1 for p in range(2) for i in
ind.genotype(chroms = [0],
ploidy = p)
if i == 1])
if ind.sex() == sim.FEMALE:
# Chromosome X
genotype += len([1 for p in range(2) for i in
ind.genotype(chroms = [1],
ploidy = p)
if i == 1])
self.assertAlmostEqual(ind.fitness, f[genotype])
else:
# Chromosome X
genotype += len([1 for i in
ind.genotype(chroms = [1],
ploidy = 0)
if i == 1])
# Chromosome Y
genotype += len([1 for i in
ind.genotype(chroms = [2],
ploidy = 1)
if i == 1])
self.assertAlmostEqual(ind.fitness, m[genotype])
