Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 1,833 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 45 46 47 | #!/usr/bin/env python
"""Load PRISM drug sensitivity data into GE database (bridge tables)."""
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 PRISM 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("--compound-meta", type=str, default=None, help="Repurposing Hub sample sheet")
parser.add_argument("--primary-file", type=str, default=None)
parser.add_argument("--secondary-file", type=str, default=None)
parser.add_argument("--release", type=str, default="PRISM_24Q2")
args = parser.parse_args()
from negbiodb_depmap.etl_prism import load_prism_compounds, load_prism_sensitivity
db_path = Path(args.db_path) if args.db_path else _PROJECT_ROOT / "data" / "negbiodb_depmap.db"
# Load compounds
if args.compound_meta:
stats = load_prism_compounds(db_path, Path(args.compound_meta))
print("\nPRISM compound loading:")
for k, v in stats.items():
print(f" {k}: {v:,}" if isinstance(v, int) else f" {k}: {v}")
# Load sensitivity
primary = Path(args.primary_file) if args.primary_file else None
secondary = Path(args.secondary_file) if args.secondary_file else None
if primary or secondary:
stats = load_prism_sensitivity(
db_path, primary_file=primary, secondary_file=secondary,
depmap_release=args.release,
)
print("\nPRISM sensitivity loading:")
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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