skills/alphagenome/scripts/_common.py

• VariantSpec · class · L110-L134 — class VariantSpec
• str · method · L119-L120 — def str(self) -> str
• is_snv · method · L123-L124 — def is_snv(self) -> bool
• to_row · method · L126-L134 — def to_row(self) -> dict[str, object]
• normalize_chromosome · function · L137-L150 — def normalize_chromosome(contig: str) -> str
• parse_variant_string · function · L164-L187 — def parse_variant_string(text: str, name: str = "") -> VariantSpec
• parse_interval_string · function · L190-L205 — def parse_interval_string(text: str) -> tuple[str, int, int]
• interval_width · function · L208-L209 — def interval_width(start0: int, end: int) -> int
• _split_delimited · function · L212-L229 — def _split_delimited(path: Path) -> tuple[list[str], list[list[str]]]
• read_vcf · function · L235-L268 — def read_vcf(path: Path) -> tuple[list[VariantSpec], list[str]]
• read_variant_table · function · L271-L335 — def read_variant_table(path: str | Path) -> tuple[list[VariantSpec], list[str]]
• column · function · L292-L296 — def column(*names: str) -> int | None
• collect_variants · function · L338-L351 — def collect_variants( variant_args: Sequence[str] | None, input_path: str | None, ) -> tuple[list[VariantSpec], list[str]]
• load_api_key · function · L359-L375 — def load_api_key(env_var: str | None = None) -> str
• require_alphagenome · function · L378-L385 — def require_alphagenome()
• cdf_to_tail_and_phred · function · L393-L404 — def cdf_to_tail_and_phred(cdf_quantile: float, floor: float = 1e-7) -> tuple[float, float]
• phred_to_top_percent · function · L407-L411 — def phred_to_top_percent(phred: float) -> float
• feature_display_name · function · L414-L416 — def feature_display_name(key: str) -> str
• portal_variant_url · function · L419-L427 — def portal_variant_url(variant: str) -> str
• _stringify · function · L437-L444 — def _stringify(value: object) -> object
• write_rows · function · L447-L489 — def write_rows( rows: Sequence[Mapping[str, object]], output: str | None, fmt: str = "tsv", columns: Sequence[str] | None = None, ) -> None
• warn · function · L492-L493 — def warn(message: str) -> None
• format_from_output · function · L496-L506 — def format_from_output(output: str | None, explicit: str | None) -> str
• chunked · function · L509-L511 — def chunked(items: Sequence, size: int) -> Iterable[Sequence]