def test_x_affected_homozygote_male():
"""Test an affected homozygote male"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT': '1/1'})
assert check_X_dominant(variant=homozygote_variant, family=family) == True
def test_x_healthy_female_ref_call():
"""Test an healthy female ref call"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t1\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT': '0/0'})
assert check_X_dominant(variant=homozygote_variant, family=family) == True
def test_x_healthy_recessive_male():
"""Test a healthy recessive male
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t1\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '0/1'})
assert check_X_dominant(variant=recessive_variant, family=family) == False
def test_x_affected_male_ref_call():
"""Test an affected ref call male"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT': '0/0'})
assert check_X_recessive(variant=homozygote_variant,
family=family) == False
def test_x_affected_recessive_female():
"""Test a sick heterozygote female
Females needs to bo hom alt to follow pattern
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t2\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '0/1'})
assert check_X_recessive(variant=recessive_variant, family=family) == False
def test_x_affected_no_call_male():
"""Test a sick male with no gt call
This should be true since there is no information that contradicts the model
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
no_call_variant = {'genotypes': {}}
no_call_variant['genotypes']['proband'] = Genotype(**{'GT': './.'})
assert check_X_recessive(variant=no_call_variant, family=family) == True
def test_recessive_affected_het_male():
"""Test a sick male
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '0/1'})
assert check_recessive(variant=recessive_variant,
family=family,
strict=False) == False
def test_dominant_healthy_recessive_male_reduced_penetrance():
"""Test a healthy heterozygote female
Females needs to bo hom alt to follow pattern
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t1\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '0/1'})
recessive_variant['reduced_penetrance'] = True
assert check_dominant(variant=recessive_variant, family=family) == True
def test_dominant_affected_no_call_male_strict():
"""Test a sick male with no gt call
This should not be true since we allways need 'proof'
for an inheritance pattern if strict mode.
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
no_call_variant = {'genotypes': {}}
no_call_variant['genotypes']['proband'] = Genotype(**{'GT': './.'})
assert check_dominant(variant=no_call_variant, family=family,
strict=True) == False