skills/alphagenome/scripts/atlas_query.py

• _obs_variant_strings · function · L67-L70 — def _obs_variant_strings(adata) -> list[str]
• _feature_names · function · L73-L76 — def _feature_names(adata) -> list[str]
• _layer · function · L79-L83 — def _layer(adata, name: str)
• summarize_avi · function · L86-L140 — def summarize_avi(avi_adata, fi_adata=None) -> list[dict[str, Any]]
• tidy_atlas_scores · function · L143-L187 — def tidy_atlas_scores(scores: Mapping[str, Any]) -> list[dict[str, Any]]
• max_abs_track · function · L190-L208 — def max_abs_track(adata) -> dict[str, Any] | None
• scorer_rows · function · L211-L225 — def scorer_rows(metadata: Mapping[str, Any]) -> list[dict[str, Any]]
• track_rows · function · L228-L246 — def track_rows(metadata: Mapping[str, Any], scorer: str | None, query: str | None) -> list[dict[str, Any]]
• make_client · function · L254-L266 — def make_client(args: argparse.Namespace)
• to_genome_variant · function · L269-L278 — def to_genome_variant(spec: common.VariantSpec)
• to_genome_interval · function · L281-L291 — def to_genome_interval(text: str, max_window: int)
• _query_each · function · L294-L313 — def _query_each( client, specs: Sequence[common.VariantSpec], requested_scorers: Sequence[str], workers: int, **filters: Any, ) -> list[tuple[common.VariantSpec, Mapping[str, Any] | None, str]]
• one · function · L303-L308 — def one(spec: common.VariantSpec)
• cmd_avi · function · L321-L397 — def cmd_avi(args: argparse.Namespace) -> int
• cmd_scores · function · L400-L435 — def cmd_scores(args: argparse.Namespace) -> int
• cmd_scorers · function · L438-L442 — def cmd_scorers(args: argparse.Namespace) -> int
• cmd_tracks · function · L445-L453 — def cmd_tracks(args: argparse.Namespace) -> int
• _add_common · function · L461-L466 — def _add_common(parser: argparse.ArgumentParser) -> None
• _add_variant_inputs · function · L469-L474 — def _add_variant_inputs(parser: argparse.ArgumentParser) -> None
• build_parser · function · L477-L513 — def build_parser() -> argparse.ArgumentParser
• main · function · L516-L518 — def main(argv: Sequence[str] | None = None) -> int