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3e219fa | 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 | """Pre-warm the gnomAD SQLite cache for a list of variants.
The gnomAD GraphQL API is open but slow under sustained load. For batch
classification runs (eval set, day-1 lab variant pull), pre-fetching every
variant ID into the local SQLite cache (`data/gnomad_cache.db`) keeps the
critical-path classification under 30s per variant.
Input
-----
A text file with one gnomAD variant ID per line (format: `chr-pos-ref-alt`,
no `chr` prefix). Lines starting with `#` are skipped.
Usage
-----
python -m scripts.warm_gnomad_cache variant_ids.txt
"""
from __future__ import annotations
import argparse
import asyncio
import logging
import sys
from pathlib import Path
from backend.app.services.gnomad import GnomADClient
logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
logger = logging.getLogger("warm_gnomad")
async def warm(ids: list[str], concurrency: int) -> None:
client = GnomADClient()
sem = asyncio.Semaphore(concurrency)
async def one(vid: str) -> None:
async with sem:
try:
freq = await client.lookup(vid)
logger.info(
"%s — AF=%s, hom=%s",
vid,
f"{freq.overall_af:.2e}" if freq.overall_af else "—",
freq.homozygote_count or 0,
)
except Exception as e:
logger.warning("%s failed: %s", vid, e)
await asyncio.gather(*(one(v) for v in ids))
def main() -> int:
parser = argparse.ArgumentParser()
parser.add_argument("ids_file", type=Path, help="One variant ID per line (chr-pos-ref-alt)")
parser.add_argument("--concurrency", type=int, default=4, help="Parallel requests (gnomAD rate-limits)")
args = parser.parse_args()
if not args.ids_file.exists():
logger.error("file not found: %s", args.ids_file)
return 1
raw = args.ids_file.read_text().splitlines()
ids = [ln.strip() for ln in raw if ln.strip() and not ln.startswith("#")]
logger.info("warming %d variants with concurrency=%d", len(ids), args.concurrency)
asyncio.run(warm(ids, args.concurrency))
return 0
if __name__ == "__main__":
sys.exit(main())
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