Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 1,560 Bytes
6d1bbc7 | 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 | #!/usr/bin/env python
"""Load DepMap CRISPR data into GE database."""
import argparse
from pathlib import Path
_PROJECT_ROOT = Path(__file__).resolve().parent.parent
_DEFAULT_DATA = _PROJECT_ROOT / "data" / "depmap_raw"
def main():
parser = argparse.ArgumentParser(description="Load DepMap CRISPR data into GE DB")
parser.add_argument("--db-path", type=str, default=None)
parser.add_argument("--data-dir", type=str, default=str(_DEFAULT_DATA))
parser.add_argument("--release", type=str, default="25Q3")
parser.add_argument("--chunk-size", type=int, default=100)
parser.add_argument("--batch-size", type=int, default=5000)
args = parser.parse_args()
from negbiodb_depmap.etl_depmap import load_depmap_crispr
data_dir = Path(args.data_dir)
db_path = Path(args.db_path) if args.db_path else None
stats = load_depmap_crispr(
db_path=db_path or _PROJECT_ROOT / "data" / "negbiodb_depmap.db",
gene_effect_file=data_dir / "CRISPRGeneEffect.csv",
dependency_file=data_dir / "CRISPRGeneDependency.csv",
model_file=data_dir / "Model.csv",
essential_file=data_dir / "AchillesCommonEssentialControls.csv",
nonessential_file=data_dir / "AchillesNonessentialControls.csv",
depmap_release=args.release,
chunk_size=args.chunk_size,
batch_size=args.batch_size,
)
print("\nDepMap CRISPR ETL complete:")
for k, v in stats.items():
print(f" {k}: {v:,}" if isinstance(v, int) else f" {k}: {v}")
if __name__ == "__main__":
main()
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