def insert_snv_variants(adapter: MongoAdapter, case_obj: Case) -> None:
"""Build variant documents and bulk insert them into database"""
variants = []
for variant in VCF(case_obj.vcf_path, threads=settings.cyvcf_threads):
variant_id = get_variant_id(variant=variant)
ref = variant.REF
alt = variant.ALT[0]
coordinates = get_coords(variant)
chrom = coordinates["chrom"]
pos = coordinates["pos"]
found_homozygote = 0
found_hemizygote = 0
for ind_obj in case_obj.individuals:
ind_pos = ind_obj["ind_index"]
if int(variant.gt_quals[ind_pos]) < settings.load_gq_threshold:
continue
genotype = GENOTYPE_MAP[variant.gt_types[ind_pos]]
if genotype not in ["het", "hom_alt"]:
continue
if genotype == "hom_alt":
found_homozygote = 1
if (
chrom in ["X", "Y"]
and ind_obj["sex"] == 1
and not check_par(chrom, pos, genome_build=settings.genome_build)
):
found_hemizygote = 1
variant_obj = Variant(
variant_id=variant_id,
chrom=chrom,
pos=pos,
end=coordinates["end"],
ref=ref,
alt=alt,
end_chrom=coordinates["end_chrom"],
sv_type=coordinates["sv_type"],
sv_len=coordinates["sv_length"],
case_id=case_obj.case_id,
homozygote=found_homozygote,
hemizygote=found_hemizygote,
is_sv=False,
id_column=variant.ID,
)
variants.append(variant_obj)
adapter.add_variants(variants=variants)
def test_par_region_X_lower():
chrom = 'X'
pos = 60001
assert check_par(chrom, pos)
def test_par_region_Y_second():
chrom = 'Y'
pos = 59034050
assert check_par(chrom, pos)
def test_par_region_Y_upper():
chrom = 'Y'
pos = 2649520
assert check_par(chrom, pos)
def test_par_region_Y_middle():
chrom = 'Y'
pos = 1000000
assert check_par(chrom, pos)
def test_par_region_Y_lower():
chrom = 'Y'
pos = 10001
assert check_par(chrom, pos)
def test_par_wrong_chrom():
chrom = '1'
pos = 60000
assert not check_par(chrom, pos)
def test_non_par_X_region():
chrom = 'X'
pos = 60000
assert not check_par(chrom, pos)
def test_par_region_X_second():
chrom = 'X'
pos = 154931044
assert check_par(chrom, pos)
def test_par_region_X_upper():
chrom = "X"
pos = 2649520
assert check_par(chrom, pos)
def test_par_region_X_middle():
chrom = "X"
pos = 1000000
assert check_par(chrom, pos)
