| """Species overlap between splits (S__ tags of the kept windows): how many of a split's species also occur in train. |
| |
| python species_overlap.py [--root .] [--splits heldout valid] [--ref train] |
| """ |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| import re |
| from pathlib import Path |
|
|
|
|
| def species(root: Path, split: str) -> dict[str, int]: |
| """species -> bases in the split's selected windows.""" |
| sel_path = root / split / "selected.json" |
| sel = json.loads(sel_path.read_text())["shards"] if sel_path.exists() else None |
| out: dict[str, int] = {} |
| for jl in sorted((root / split).glob("*/*.jsonl")): |
| rows = [json.loads(line) for line in jl.read_text().splitlines()] |
| ids = sel.get(str(jl.with_suffix("").relative_to(root)), []) if sel is not None else range(len(rows)) |
| for i in ids: |
| m = re.search(r"S__([^;|]*)", rows[i]["tag"]) |
| if m: |
| out[m.group(1)] = out.get(m.group(1), 0) + rows[i]["len"] |
| return out |
|
|
|
|
| def main() -> None: |
| ap = argparse.ArgumentParser() |
| ap.add_argument("--root", type=Path, default=Path(".")) |
| ap.add_argument("--splits", nargs="+", default=["heldout", "valid"]) |
| ap.add_argument("--ref", default="train") |
| a = ap.parse_args() |
| ref = species(a.root, a.ref) |
| for split in a.splits: |
| sp = species(a.root, split) |
| shared = set(sp) & set(ref) |
| tagged = sum(sp.values()) |
| print(f"{split}: {len(sp)} species, {len(shared)} also in {a.ref} " |
| f"({sum(sp[s] for s in shared) / max(tagged, 1):.1%} of its tagged bases)") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
