Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 4,533 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 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 | #!/usr/bin/env python
"""Download DepMap data files for GE domain.
Downloads from DepMap portal API and Figshare:
- CRISPRGeneEffect.csv (Chronos scores)
- CRISPRGeneDependency.csv (dependency probability)
- Model.csv (cell line metadata)
- AchillesCommonEssentialControls.csv
- AchillesNonessentialControls.csv
- D2_combined_gene_dep_scores.csv (DEMETER2 RNAi)
- Omics files (expression, CN, mutations)
Uses the DepMap download API to resolve file URLs dynamically.
"""
import argparse
import csv
import io
import sys
from pathlib import Path
import requests
_PROJECT_ROOT = Path(__file__).resolve().parent.parent
_DEFAULT_OUTPUT = _PROJECT_ROOT / "data" / "depmap_raw"
DEPMAP_FILES_API = "https://depmap.org/portal/api/download/files"
# Files to download from DepMap portal
DEPMAP_TARGET_FILES = [
"CRISPRGeneEffect.csv",
"CRISPRGeneDependency.csv",
"Model.csv",
"AchillesCommonEssentialControls.csv",
"AchillesNonessentialControls.csv",
"OmicsExpressionProteinCodingGenesTPMLogp1.csv",
"OmicsCNGene.csv",
"OmicsSomaticMutationsMatrixDamaging.csv",
]
DEMETER2_URL = "https://ndownloader.figshare.com/files/13515395" # D2_combined_gene_dep_scores.csv
def resolve_depmap_urls(target_files: list[str]) -> dict[str, str]:
"""Fetch signed download URLs from the DepMap portal API.
The API returns a CSV with columns: release, release_date, filename, url, md5_hash.
We take the first (most recent) URL for each target file.
"""
print("Fetching download URLs from DepMap portal API...")
resp = requests.get(DEPMAP_FILES_API, timeout=60)
resp.raise_for_status()
targets_remaining = set(target_files)
urls: dict[str, str] = {}
reader = csv.DictReader(io.StringIO(resp.text))
for row in reader:
fname = row.get("filename", "")
if fname in targets_remaining:
urls[fname] = row["url"]
targets_remaining.discard(fname)
if not targets_remaining:
break
if targets_remaining:
print(f" WARNING: Could not find URLs for: {targets_remaining}")
print(f" Resolved {len(urls)}/{len(target_files)} file URLs\n")
return urls
def download_file(url: str, output_path: Path, force: bool = False) -> bool:
"""Download a file with progress reporting."""
if output_path.exists() and not force:
print(f" SKIP (exists): {output_path.name}")
return False
print(f" Downloading: {output_path.name}...")
resp = requests.get(url, stream=True, timeout=600)
resp.raise_for_status()
total = int(resp.headers.get("content-length", 0))
downloaded = 0
with open(output_path, "wb") as f:
for chunk in resp.iter_content(chunk_size=1024 * 1024):
f.write(chunk)
downloaded += len(chunk)
if total:
pct = downloaded / total * 100
print(f"\r {downloaded / 1e6:.1f} MB / {total / 1e6:.1f} MB ({pct:.0f}%)", end="")
print(f"\n Done: {output_path.name} ({output_path.stat().st_size / 1e6:.1f} MB)")
return True
def main():
parser = argparse.ArgumentParser(description="Download DepMap data files")
parser.add_argument("--output-dir", type=str, default=str(_DEFAULT_OUTPUT))
parser.add_argument("--force", action="store_true", help="Re-download existing files")
parser.add_argument("--skip-omics", action="store_true", help="Skip large omics files")
parser.add_argument("--skip-rnai", action="store_true", help="Skip DEMETER2 RNAi file")
args = parser.parse_args()
output_dir = Path(args.output_dir)
output_dir.mkdir(parents=True, exist_ok=True)
print(f"Downloading DepMap files to {output_dir}\n")
# Resolve URLs from DepMap API
targets = [f for f in DEPMAP_TARGET_FILES
if not (args.skip_omics and f.startswith("Omics"))]
url_map = resolve_depmap_urls(targets)
for filename in targets:
if filename not in url_map:
print(f" SKIP (no URL): {filename}")
continue
try:
download_file(url_map[filename], output_dir / filename, force=args.force)
except Exception as e:
print(f" ERROR: {filename}: {e}")
if not args.skip_rnai:
try:
download_file(DEMETER2_URL, output_dir / "D2_combined_gene_dep_scores.csv", force=args.force)
except Exception as e:
print(f" ERROR: DEMETER2: {e}")
print("\nDownload complete.")
if __name__ == "__main__":
main()
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