skills/waypoint-bio/scripts/profiler_to_waypoint.py

• normalise_lineage · function · L73-L100 — def normalise_lineage(lineage: str) -> str
• deepest_rank · function · L103-L113 — def deepest_rank(lineage: str) -> str | None
• parse_metaphlan · function · L121-L161 — def parse_metaphlan(path: Path, rank: str) -> pd.DataFrame
• parse_kraken_report · function · L164-L214 — def parse_kraken_report(path: Path, rank: str) -> pd.Series
• parse_kraken · function · L217-L227 — def parse_kraken(paths: list[Path], rank: str) -> pd.DataFrame
• parse_table · function · L230-L273 — def parse_table( path: Path, *, taxonomy_column: str | None, orientation: str, ) -> pd.DataFrame
• matrix_to_waypoint · function · L281-L325 — def matrix_to_waypoint( matrix: pd.DataFrame, *, normalize: bool = True, drop_zeros: bool = True, min_abundance: float = 0.0, ) -> pd.DataFrame
• attach_metadata · function · L328-L347 — def attach_metadata(frame: pd.DataFrame, metadata_path: Path) -> pd.DataFrame
• build_matrix · function · L355-L370 — def build_matrix(args: argparse.Namespace, paths: list[Path]) -> pd.DataFrame
• main · function · L373-L477 — def main(argv: list[str] | None = None) -> int