def get_genotypes(variant, individuals):
"""Create genotype objects
Create Genotype objects for all individuals and return them in a
dictionary
Args:
variant (dict): A variant dict
individuals (list): A list with strings that are individual id:s
Returns:
genotype_dict (dict): A dictionary with individual id:s as strings
and Genptype objects as keys
"""
gt_format = variant.get('FORMAT', '').split(':')
genotype_dict = {}
for individual in individuals:
gt_info = variant[individual].split(':')
gt_call = dict(zip(gt_format, gt_info))
#Create a genotype object for this individual
genotype_dict[individual] = Genotype(**gt_call)
return genotype_dict
def test_family_one_affected():
"""Test healthy parents and an affected proband
"""
# family = get_family(family_file=FAMILY_FILE)
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\tfather\tmother\t1\t2\n", "1\tmother\t0\t0\t2\t1\n",
"1\tfather\t0\t0\t1\t1\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '1/1'})
recessive_variant['genotypes']['father'] = Genotype(**{'GT': '0/1'})
recessive_variant['genotypes']['mother'] = Genotype(**{'GT': '0/0'})
assert check_recessive(variant=recessive_variant,
family=family,
strict=False) == True
def test_x_affected_homozygote_female():
"""Test an affected homozygote male"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t2\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT': '1/1'})
assert check_X_recessive(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_recessive(variant=recessive_variant, family=family) == False
def test_dominant_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_dominant(variant=homozygote_variant, family=family) == False
def test_dominant_affected_recessive_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_dominant(variant=recessive_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_homozygote_male():
"""Test an healthy homozygote male"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t1\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) == 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_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
