def matched_variants() -> List[Tuple[Variant, Dict[str, str]]]:
return [
# snp
(
Variant("22", 29083907, 29083907, "G", "A", id="VCV000422506.2"),
{
"symbol": "CHEK2",
"hgvs_c": "NM_007194.4:c.1610C>T"
},
),
# deletion
(
Variant("22", 50967717, 50967719, "AGG", "A", id="VCV000223079.1"),
{
"symbol": "TYMP",
"hgvs_c": "NM_001953.4:c.263_264del"
},
),
# indel
(
Variant("22", 51065766, 51065767, "GA", "AG", id="VCV000003062.1"),
{
"symbol": "ARSA",
"hgvs_c": "NM_001085428.2:c.34_35delTCinsCT"
},
),
]
def test_variant_is_deletion(
snp: Variant, insertion: Variant, deletion: Variant, sv: Variant
):
assert not snp.is_deletion()
assert not insertion.is_deletion()
assert deletion.is_deletion()
assert not sv.is_deletion()
def test_warn_ref_mismatch(clinvar_tabix, caplog):
# wrong ref should still match the clinvar but with a warning
cols = clinvar_tabix.header[0][len("#"):].split("\t")
v_wrong_ref = Variant("22", 29083907, 29083907, "C", "A")
record = CharGer._match_clinvar_one_variant(v_wrong_ref, clinvar_tabix,
cols)
assert record is not None
assert ("got a clinvar match but their reference alleles are different"
in caplog.text)
def not_found_variants() -> List[Variant]:
return [
Variant("22", 29083907, 29083907, "G", "T"),
Variant("22", 50967718, 50967719, "GG", "G"),
Variant("22", 51065766, 51065767, "GA", "C"),
]
def grch38_vep95_annotated_variants_info_fixed(test_root: Path) -> List[Variant]:
return list(
Variant.read_and_parse_vcf(
test_root.joinpath("examples/grch38_vep95_50_variants.info_fixed.vcf.gz")
)
)
def grch37_vep85_annotated_variants(test_root: Path):
return list(
Variant.read_and_parse_vcf(
test_root / "examples" / "grch37_vep85_5_variants.vcf"
)
)
def sv() -> Variant:
return Variant("1", 2827693, 2827701, "CCCCTCGCA", "C", info={"SVTYPE": "DEL"})
def deletion() -> Variant:
return Variant("1", 42, 44, "ATA", "A")
def insertion() -> Variant:
return Variant("1", 42, 42, "A", "ATAT")
def snp() -> Variant:
return Variant("1", 42, 42, "A", "G")
def test_read_vcf_detect_vep_version(
test_root: Path, caplog, vcf_pth: Path, vep_ver: int
):
reader = Variant.read_and_parse_vcf(test_root.joinpath(vcf_pth))
next(reader)
assert f"VEP version {vep_ver}" in caplog.text
def charger_result(test_root: Path):
variant = next(
Variant.read_and_parse_vcf(test_root / "examples" /
"grch37_vep85_5_variants.vcf"))
return CharGerResult(variant)