def setup_80freq():
pop = Population()
for i in range(600):
ind = pop.founder_individual()
ind.genotypes = [[[1], [1]]]
for i in range(400):
ind = pop.founder_individual()
ind.genotypes = [[[2], [1]]]
return pop
def setup_80freq():
pop = Population()
for i in range(600):
ind = pop.founder_individual()
ind.genotypes = [ [ [1],[1] ] ]
for i in range(400):
ind = pop.founder_individual()
ind.genotypes = [ [ [2],[1] ] ]
return pop
def test_major_allele():
pop = Population()
# 2000 A alleles
for x in range(1000):
ind = pop.founder_individual()
ind.genotypes = [(Alleles([1]), Alleles([1]))]
# 500 A alleles, 500 B
for x in range(500):
ind = pop.founder_individual()
ind.genotypes = [(Alleles([1]), Alleles([2]))]
assert pop.major_allele((0, 0)) == 1
def test_allele_list():
pop = Population()
loc = 0, 0
# 2000 A alleles
for x in range(1000):
ind = pop.founder_individual()
ind.genotypes = [(Alleles([1]), Alleles([1]))]
# 500 A alleles, 500 B
for x in range(500):
ind = pop.founder_individual()
ind.genotypes = [(Alleles([1]), Alleles([2]))]
assert sorted(pop.allele_list(loc)) == [1] * 2500 + [2] * 500
def test_major_allele():
pop = Population()
# 2000 A alleles
for x in range(1000):
ind = pop.founder_individual()
ind.genotypes = [ (Alleles([1]), Alleles([1]) )]
# 500 A alleles, 500 B
for x in range(500):
ind = pop.founder_individual()
ind.genotypes = [ (Alleles([1]), Alleles([2]) )]
assert pop.major_allele((0,0)) == 1
def test_allele_list():
pop = Population()
loc = 0,0
# 2000 A alleles
for x in range(1000):
ind = pop.founder_individual()
ind.genotypes = [ (Alleles([1]), Alleles([1]) )]
# 500 A alleles, 500 B
for x in range(500):
ind = pop.founder_individual()
ind.genotypes = [ (Alleles([1]), Alleles([2]) )]
assert sorted(pop.allele_list(loc)) == [1]*2500 + [2]*500
def test_ld():
# Data from Hartl & Clark, Table 2.2 (pg 85)
haplotypes = chain([Alleles(['A','B'])] * 25,
[Alleles(['A','b'])] * 475, [Alleles(['a','B'])] * 475,
[Alleles(['a','b'])] * 9025)
pop = Population()
for chroms in grouper(haplotypes,2):
ind = pop.founder_individual()
ind.genotypes = [chroms]
known_D = 0
assert pop.ld( (0,0), (0,1), method='D') == known_D