File size: 2,685 Bytes
d11f31d | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | """Download and prepare the filtered K562 and RPE1 datasets used by CausalBench."""
import argparse
from pathlib import Path
import subprocess
import numpy as np
import pandas as pd
from upstream.preprocessing import preprocess_dataset
ROOT = Path(__file__).resolve().parent
RAW = ROOT / "data/raw"
DATASETS = {
"k562": (35773219, "TabB_K562_day6_summary_stat"),
"rpe1": (35775606, "TabC_RPE1_summary_statistic"),
}
SUMMARY_URL = "https://ars.els-cdn.com/content/image/1-s2.0-S0092867422005979-mmc2.xlsx"
def download(url, path):
if path.exists():
return path
path.parent.mkdir(parents=True, exist_ok=True)
partial = path.with_suffix(path.suffix + ".part")
subprocess.run(
["curl", "--fail", "--location", "--retry", "3", "--continue-at", "-",
"--output", str(partial), url],
check=True,
)
partial.replace(path)
return path
def prepare(name, output_dir):
npz = output_dir / f"dataset_{name}_filtered.npz"
tsv = output_dir / f"causalbench_{name}.tsv.gz"
if npz.exists() and tsv.exists():
print(f"{name}: using existing files in {output_dir}")
return
if npz.exists() or tsv.exists():
raise FileExistsError("Output is incomplete. Choose a new --output-dir to rebuild.")
_, sheet = DATASETS[name]
summary = pd.read_excel(RAW / "summary_stats.xlsx", sheet_name=sheet)
expression, genes, labels = preprocess_dataset(str(RAW / f"{name}.h5ad"), summary)
output_dir.mkdir(parents=True, exist_ok=True)
np.savez(npz, expression_matrix=expression, var_names=np.asarray(genes, dtype=str),
interventions=np.asarray(labels, dtype=str))
table = pd.DataFrame(expression, columns=genes)
table["intervention"] = labels
table.to_csv(tsv, sep="\t", index=False, compression="gzip")
print(f"{name}: saved {expression.shape[0]:,} cells × {expression.shape[1]} genes")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("dataset", choices=["k562", "rpe1", "all"], nargs="?", default="all")
parser.add_argument("--download-only", action="store_true")
parser.add_argument("--output-dir", type=Path, default=ROOT / "data/prepared")
args = parser.parse_args()
names = DATASETS if args.dataset == "all" else [args.dataset]
download(SUMMARY_URL, RAW / "summary_stats.xlsx")
for name in names:
file_id, _ = DATASETS[name]
download(f"https://ndownloader.figshare.com/files/{file_id}", RAW / f"{name}.h5ad")
if args.download_only:
print(f"{name}: raw data ready in {RAW}")
else:
prepare(name, args.output_dir)
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