def test_nocall():
"""A nocall is when no informations is found on this position for the individual. It should be False on all questions except nocall. Also in the case of haploidity the result should be the same."""
my_nocall = genotype.Genotype('./.')
my_short_nocall = genotype.Genotype('.')
assert my_nocall.genotype == './.' #We never need to look at the alleles since genotype is defined by 'allele_1/allele_2'
assert my_short_nocall.genotype == './.'
assert not my_nocall.heterozygote
assert not my_short_nocall.heterozygote
assert not my_nocall.homo_ref
assert not my_short_nocall.homo_ref
assert not my_nocall.homo_alt
assert not my_short_nocall.homo_alt
assert not my_nocall.has_variant
assert not my_short_nocall.has_variant
assert not my_nocall.genotyped
assert not my_short_nocall.genotyped
def test_homo_ref():
"""A homozygote reference call. has_variant and nocall is False and homo_ref is true."""
my_homo_ref_genotype = genotype.Genotype('0/0')
assert my_homo_ref_genotype.genotype == '0/0'
assert not my_homo_ref_genotype.heterozygote
assert my_homo_ref_genotype.homo_ref
assert not my_homo_ref_genotype.homo_alt
assert not my_homo_ref_genotype.has_variant
assert my_homo_ref_genotype.genotyped
def test_genotype_1_2():
"""docstring for test_genotype_1_2. A normal heterozygote call, has_variant and heterozygote is true."""
my_genotype = genotype.Genotype('1/2')
assert my_genotype.genotype == '1/2'
assert my_genotype.heterozygote
assert not my_genotype.homo_ref
assert not my_genotype.homo_alt
assert my_genotype.has_variant
assert my_genotype.genotyped
def test_genotype_0():
"""The vcf format allows calls that look like '0'. This is a haploid call and should be treated as Homozygote Reference."""
my_genotype = genotype.Genotype('0')
assert my_genotype.genotype == '0/.'
assert not my_genotype.heterozygote
assert my_genotype.homo_ref
assert not my_genotype.homo_alt
assert not my_genotype.has_variant
assert my_genotype.genotyped
def test_genotype_1():
"""The vcf format allows calls that look like '1'. This is a haploid call and should be treated as Homozygote Alternative."""
my_genotype = genotype.Genotype('1')
assert my_genotype.genotype == '1/.'
assert not my_genotype.heterozygote
assert not my_genotype.homo_ref
assert my_genotype.homo_alt
assert my_genotype.has_variant
assert my_genotype.genotyped
def test_homo_alt_2():
"""A homozygote alternative call. has_variant and homo_alt is true."""
my_genotype = genotype.Genotype('3/3')
assert my_genotype.genotype == '3/3'
assert not my_genotype.heterozygote
assert not my_genotype.homo_ref
assert my_genotype.homo_alt
assert my_genotype.has_variant
assert my_genotype.genotyped
def test_phased_data():
"""Try if the class van handle phased data. In this case a heterozygote."""
my_genotype = genotype.Genotype('1|0')
assert my_genotype.genotype == '1/0' # If asked about the genotype, it should still be on the same form.
assert my_genotype.heterozygote
assert not my_genotype.homo_ref
assert not my_genotype.homo_alt
assert my_genotype.has_variant
assert my_genotype.allele_1 == '1' # If asked about the genotype, it should still be on the same form.
assert my_genotype.allele_2 == '0' # If asked about the genotype, it should still be on the same form.
assert my_genotype.genotyped