[docs]
def cnv_variant_type(variant_type: str) -> str | None:
variant = variant_type.lower()
if variant in {"cnv+", "duplication", "large_insertion", "gain"}:
return "LARGE_DUPLICATION"
if variant in {"cnv-", "deletion", "large_deletion", "loss"}:
return "LARGE_DELETION"
return None
[docs]
def cshl2cnv_variant(location: str, variant: str) -> tuple[str, int, int, str]:
# pylint: disable=unused-argument
"""Parse location and variant into CNV variant."""
parts = location.split(":")
if len(parts) != 2:
raise ValueError(
f"unexpected location format: "
f"location={location}, variant=f{variant}")
chrom, pos_range = parts
parts = pos_range.split("-")
if len(parts) != 2:
raise ValueError(
f"unexpected location format: "
f"location={location}, variant=f{variant}")
pos_begin, pos_end = parts
variant_type = cnv_variant_type(variant)
if variant_type is None:
raise ValueError(f"unexpected CNV variant type: {variant}")
return chrom, int(pos_begin), int(pos_end), variant_type