def test_seqalleles():
chroms = [blank_chromosome(2) for x in range(2)]
seqalleles = '1 2 1 1 2 2 2 1'.split()
gts = genotypes_from_sequential_alleles(chroms, seqalleles)
# Test to make sure the types returned are correct
assert all(type(x) is Alleles for x in chain.from_iterable(gts))
# Test to make sure the values are correct
assert (gts[0][0] == ['1','1']).all()
assert (gts[0][1] == ['2','1']).all()
assert (gts[1][0] == ['2','2']).all()
assert (gts[1][1] == ['2','1']).all()
def test_seqalleles():
chroms = [blank_chromosome(2) for x in range(2)]
seqalleles = '1 2 1 1 2 2 2 1'.split()
gts = genotypes_from_sequential_alleles(chroms, seqalleles)
# Test to make sure the types returned are correct
assert all(type(x) is Alleles for x in chain.from_iterable(gts))
# Test to make sure the values are correct
assert (gts[0][0] == ['1','1']).all()
assert (gts[0][1] == ['2','1']).all()
assert (gts[1][0] == ['2','2']).all()
assert (gts[1][1] == ['2','1']).all()
def data_handler(ind, data):
# Handle the phenotypes first
phendata = data[phenotype_indices]
for phenotype, value in zip(phenotypes, phendata):
kind, label = phenotype
if kind == 'A':
value = True if value == '1' else False
else:
value = float(value) if '.' in value else int(value)
ind.phenotypes[label] = value
gts = data[genotype_indices]
ind.genotypes = genotypes_from_sequential_alleles(chromsomes,
gts,
missing_code='X')
def test_seqalleles_raiseforbadmissingval():
chroms = [blank_chromosome(2) for x in range(2)]
seqalleles = '1 2 1 1 2 2 2 1'.split()
gts = genotypes_from_sequential_alleles(chroms, seqalleles, missing_code=0)
def test_seqalleles_raiseforbadmissingval():
chroms = [blank_chromosome(2) for x in range(2)]
seqalleles = '1 2 1 1 2 2 2 1'.split()
gts = genotypes_from_sequential_alleles(chroms, seqalleles, missing_code=0)
def plink_data_handler(ind, data):
""" A function to handle the data payload from a plink line """
ind.genotypes = genotypes_from_sequential_alleles(ind.chromosomes, data, missing_code="0")
