def test_labelledallele_delabeler():
ngenos = 10 # Number of genotypes per chromosome
if ngenos % 2 == 1:
raise ValueError('Even number of genotypes needed')
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
a._init_genotypes(blankchroms=False)
a.genotypes[0][0] = Alleles([1]*ngenos)
a.genotypes[0][1] = Alleles([2]*ngenos)
b = Individual(p, 2)
b._init_genotypes(blankchroms=False)
b.genotypes[0][0] = Alleles([3] * ngenos)
b.genotypes[0][1] = Alleles([4] * ngenos)
chromatid_spans = [InheritanceSpan(a, 0, 0, 0, ngenos//2),
InheritanceSpan(b, 0, 1, ngenos//2, ngenos)]
chromatid = LabelledAlleles(spans=chromatid_spans, chromobj=c)
expected_value = [1]*(ngenos//2) + [4] * (ngenos//2)
expected_value = Alleles(expected_value)
actual_value = chromatid.delabel()
assert all(actual_value == expected_value)
def test_labelledallele_delabeler():
ngenos = 10 # Number of genotypes per chromosome
if ngenos % 2 == 1:
raise ValueError('Even number of genotypes needed')
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
a._init_genotypes(blankchroms=False)
a.genotypes[0][0] = Alleles([1] * ngenos)
a.genotypes[0][1] = Alleles([2] * ngenos)
b = Individual(p, 2)
b._init_genotypes(blankchroms=False)
b.genotypes[0][0] = Alleles([3] * ngenos)
b.genotypes[0][1] = Alleles([4] * ngenos)
chromatid_spans = [
InheritanceSpan(a, 0, 0, 0, ngenos // 2),
InheritanceSpan(b, 0, 1, ngenos // 2, ngenos)
]
chromatid = LabelledAlleles(spans=chromatid_spans, chromobj=c)
expected_value = [1] * (ngenos // 2) + [4] * (ngenos // 2)
expected_value = Alleles(expected_value)
actual_value = chromatid.delabel()
assert all(actual_value == expected_value)
def test_labelledalleles():
IS = InheritanceSpan
ngenos = 50
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
actual = LabelledAlleles.founder_chromosome(a, 0, 0, chromobj=c)
expected = LabelledAlleles(spans=[IS(a, 0, 0, 0, ngenos)], chromobj=c)
assert actual == expected
def test_labelledalleles():
IS = InheritanceSpan
ngenos = 50
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
actual = LabelledAlleles.founder_chromosome(a, 0, 0, chromobj=c)
expected = LabelledAlleles(spans=[IS(a, 0, 0, 0, ngenos)], chromobj=c)
assert actual == expected
def labelled_chromatids(i, c):
a = LabelledAlleles.founder_chromosome(self, i, 0, chromobj=c)
b = LabelledAlleles.founder_chromosome(self, i, 1, chromobj=c)
return (a, b)
def labelled_chromatids(i, c):
a = LabelledAlleles.founder_chromosome(self, i, 0, chromobj=c)
b = LabelledAlleles.founder_chromosome(self, i, 1, chromobj=c)
return (a, b)
