kemalandClaude Opus 5.5
2e75345a30
- tests/oracle/test_p2_raw_xy.py: IDAT-assembled raw X/Y and controls equal the arrays in oracle GTCs - validate_p1_large.py: phase-P2 comparison against vendor GTCs with diagnostics (channel swap, bead-count disagreements) - cloud trial: also runs `simurg ingest` on all samples (time/memory), disk 250 GB Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
316 lines
13 KiB
Python
316 lines
13 KiB
Python
#!/usr/bin/env python3
|
|
"""Phase P1 validation on a large data set (e.g. 1000 Genomes Omni2.5, 2141 samples with vendor GTCs).
|
|
|
|
For every GTC: parse, compare every field with Illumina BeadArrayFiles (BSD-2) and test the byte-identical
|
|
round-trip. For every IDAT pair: parse, pair-check and compare the address set with the manifest. BPM/EGT/CSV are
|
|
compared with BeadArrayFiles once. Writes a JSON summary; exit code 0 only if everything matched.
|
|
|
|
Usage: validate_p1_large.py --root DIR --bpm F --egt F [--csv F] --out summary.json [--workers N] [--limit N]
|
|
"""
|
|
|
|
from __future__ import annotations
|
|
|
|
import argparse
|
|
import json
|
|
import os
|
|
import sys
|
|
import time
|
|
import traceback
|
|
from concurrent.futures import ProcessPoolExecutor
|
|
from pathlib import Path
|
|
from typing import Any
|
|
|
|
import numpy as np
|
|
|
|
ROOT = Path(__file__).resolve().parents[1]
|
|
sys.path.insert(0, str(ROOT / "refs" / "BeadArrayFiles"))
|
|
|
|
|
|
def check_gtc(path: str) -> dict[str, Any]:
|
|
from module.GenotypeCalls import GenotypeCalls # type: ignore[import-not-found]
|
|
|
|
from simurg.formats.gtc import encode_gtc, read_gtc
|
|
|
|
res: dict[str, Any] = {"file": path, "ok": True, "diffs": []}
|
|
try:
|
|
g = read_gtc(path, check_write_complete=False)
|
|
raw = Path(path).read_bytes()
|
|
res["version"] = g.version
|
|
res["autocall_version"] = g.autocall_version
|
|
res["roundtrip_identical"] = encode_gtc(g) == raw
|
|
if not res["roundtrip_identical"]:
|
|
res["roundtrip_canonical_identical"] = encode_gtc(g, canonical=True) == raw
|
|
res["size_ours_vs_file"] = [len(encode_gtc(g)), len(raw)]
|
|
b = GenotypeCalls(path, check_write_complete=False)
|
|
pairs = {
|
|
"raw_x": (g.raw_x, b.get_raw_x_intensities()),
|
|
"raw_y": (g.raw_y, b.get_raw_y_intensities()),
|
|
"genotypes": (g.genotypes, np.array(b.get_genotypes(), dtype=np.uint8)),
|
|
"scores": (g.genotype_scores, b.get_genotype_scores()),
|
|
}
|
|
if g.version >= 4:
|
|
pairs["baf"] = (g.b_allele_freqs, b.get_ballele_freqs())
|
|
pairs["lrr"] = (g.logr_ratios, b.get_logr_ratios())
|
|
for k, (a, c) in pairs.items():
|
|
if not np.array_equal(np.asarray(a), np.asarray(c), equal_nan=a.dtype.kind == "f"):
|
|
res["diffs"].append(k)
|
|
scalars = {
|
|
"call_rate": (g.call_rate, b.get_call_rate()),
|
|
"gender": (g.gender, b.get_gender()),
|
|
"logr_dev": (g.logr_dev, b.get_logr_dev()),
|
|
"gc10": (g.gc10, b.get_gc10()),
|
|
"gc50": (g.gc50, b.get_gc50()),
|
|
"num_calls": (g.num_calls, b.get_num_calls()),
|
|
"sample_name": (g.sample_name, b.get_sample_name()),
|
|
"base_calls": (g.base_call_strings(), [x.decode() for x in b.get_base_calls()]),
|
|
}
|
|
for k, (a, c) in scalars.items():
|
|
same = (a == c) or (isinstance(a, float) and np.isnan(a) and np.isnan(c))
|
|
if not same:
|
|
res["diffs"].append(k)
|
|
xf_b = [
|
|
(t.offset_x, t.offset_y, t.scale_x, t.scale_y, t.shear, t.theta) for t in b.get_normalization_transforms()
|
|
]
|
|
xf_g = [
|
|
tuple(float(x[k]) for k in ("offset_x", "offset_y", "scale_x", "scale_y", "shear", "theta"))
|
|
for x in g.normalization_transforms
|
|
]
|
|
if [tuple(float(v) for v in t) for t in xf_b] != xf_g:
|
|
res["diffs"].append("normalization_transforms")
|
|
res["ok"] = not res["diffs"]
|
|
except Exception as e:
|
|
res.update(ok=False, error=f"{type(e).__name__}: {e}", trace=traceback.format_exc(limit=3))
|
|
return res
|
|
|
|
|
|
def check_idat_pair(args: tuple[str, str]) -> dict[str, Any]:
|
|
from simurg.formats.idat import check_pair, read_idat
|
|
|
|
grn, red = args
|
|
res: dict[str, Any] = {"grn": grn, "ok": True}
|
|
try:
|
|
g, r = read_idat(grn), read_idat(red)
|
|
check_pair(g, r)
|
|
res.update(
|
|
n=g.n_addresses,
|
|
chip=g.chip_type,
|
|
midblock_itemsize=g.mid_block_itemsize,
|
|
scan=g.scan_time_iso,
|
|
name_ok=(g.barcode in Path(grn).name),
|
|
)
|
|
except Exception as e:
|
|
res.update(ok=False, error=f"{type(e).__name__}: {e}")
|
|
return res
|
|
|
|
|
|
_P2: dict[str, Any] = {}
|
|
|
|
|
|
def _p2_init(manifest: Any) -> None:
|
|
_P2.clear()
|
|
_P2["m"] = manifest
|
|
|
|
|
|
def check_raw_xy(args: tuple[str, str, str]) -> dict[str, Any]:
|
|
"""P2: raw X/Y + controls assembled from IDATs vs the arrays stored in the GTC (TOC 1000/1001/500/501)."""
|
|
from simurg.formats.gtc import read_gtc
|
|
from simurg.formats.idat import read_idat
|
|
from simurg.signal.raw_xy import LocusMapCache, assemble_raw_xy
|
|
|
|
gtc, grn, red = args
|
|
res: dict[str, Any] = {"gtc": gtc, "ok": True}
|
|
try:
|
|
m = _P2["m"]
|
|
cache = _P2.setdefault("cache", LocusMapCache(m))
|
|
ref = read_gtc(gtc, check_write_complete=False)
|
|
raw = assemble_raw_xy(read_idat(grn), read_idat(red), m, cache=cache)
|
|
dx = raw.raw_x != ref.raw_x
|
|
dy = raw.raw_y != ref.raw_y
|
|
diff = dx | dy
|
|
res.update(
|
|
n_diff=int(diff.sum()),
|
|
n_missing=raw.n_missing,
|
|
vendor_zero=int(((ref.raw_x == 0) & (ref.raw_y == 0)).sum()),
|
|
# plan §20 U1: would swapping channels explain the differences?
|
|
swapped=int(((raw.raw_x == ref.raw_y) & (raw.raw_y == ref.raw_x) & diff).sum()),
|
|
ours_missing_vendor_nonzero=int((raw.missing & ((ref.raw_x != 0) | (ref.raw_y != 0))).sum()),
|
|
vendor_zero_ours_present=int((~raw.missing & (ref.raw_x == 0) & (ref.raw_y == 0)).sum()),
|
|
controls_equal=bool(
|
|
np.array_equal(raw.controls_x, ref.controls_x) and np.array_equal(raw.controls_y, ref.controls_y)
|
|
),
|
|
)
|
|
if res["n_diff"]:
|
|
idx = np.flatnonzero(diff)[:5].tolist()
|
|
res["examples"] = [
|
|
{
|
|
"locus": m.names[i],
|
|
"assay": int(m.assay_types[i]),
|
|
"ours": [int(raw.raw_x[i]), int(raw.raw_y[i])],
|
|
"vendor": [int(ref.raw_x[i]), int(ref.raw_y[i])],
|
|
}
|
|
for i in idx
|
|
]
|
|
res["ok"] = res["n_diff"] == 0 and res["controls_equal"]
|
|
except Exception as e:
|
|
res.update(ok=False, error=f"{type(e).__name__}: {e}")
|
|
return res
|
|
|
|
|
|
def main() -> int:
|
|
ap = argparse.ArgumentParser()
|
|
ap.add_argument("--root", required=True, type=Path)
|
|
ap.add_argument("--bpm", required=True, type=Path)
|
|
ap.add_argument("--egt", required=True, type=Path)
|
|
ap.add_argument("--csv", type=Path)
|
|
ap.add_argument("--out", required=True, type=Path)
|
|
ap.add_argument("--workers", type=int, default=os.cpu_count() or 1)
|
|
ap.add_argument("--limit", type=int, default=0)
|
|
ap.add_argument("--no-p2", action="store_true", help="skip the phase-P2 raw X/Y check")
|
|
a = ap.parse_args()
|
|
|
|
from simurg.formats.bpm import read_bpm
|
|
from simurg.formats.discovery import walk_files
|
|
from simurg.formats.egt import read_egt
|
|
|
|
t0 = time.time()
|
|
summary: dict[str, Any] = {"root": str(a.root), "started": time.strftime("%Y-%m-%dT%H:%M:%SZ", time.gmtime())}
|
|
|
|
gtcs = [str(p) for p in walk_files(a.root, (".gtc",))]
|
|
idats = walk_files(a.root, (".idat", ".idat.gz"))
|
|
if a.limit:
|
|
gtcs = gtcs[: a.limit]
|
|
grn = {p.name.lower().replace("_grn.idat", ""): p for p in idats if "_grn.idat" in p.name.lower()}
|
|
red = {p.name.lower().replace("_red.idat", ""): p for p in idats if "_red.idat" in p.name.lower()}
|
|
pairs = [(str(grn[k]), str(red[k])) for k in sorted(set(grn) & set(red))]
|
|
if a.limit:
|
|
pairs = pairs[: a.limit]
|
|
summary["n_gtc"] = len(gtcs)
|
|
summary["n_idat_pairs"] = len(pairs)
|
|
summary["unpaired_idats"] = len(set(grn) ^ set(red))
|
|
|
|
with ProcessPoolExecutor(a.workers) as ex:
|
|
gres = list(ex.map(check_gtc, gtcs, chunksize=4))
|
|
ires = list(ex.map(check_idat_pair, pairs, chunksize=8))
|
|
summary["gtc_ok"] = sum(r["ok"] for r in gres)
|
|
summary["gtc_roundtrip_identical"] = sum(bool(r.get("roundtrip_identical")) for r in gres)
|
|
summary["gtc_versions"] = sorted({r.get("version") for r in gres if "version" in r})
|
|
summary["gtc_autocall_versions"] = sorted({r.get("autocall_version") for r in gres if "autocall_version" in r})
|
|
summary["gtc_failures"] = [r for r in gres if not r["ok"]][:50]
|
|
summary["gtc_roundtrip_failures"] = [r for r in gres if r.get("roundtrip_identical") is False][:20]
|
|
summary["idat_ok"] = sum(r["ok"] for r in ires)
|
|
summary["idat_failures"] = [r for r in ires if not r["ok"]][:50]
|
|
summary["idat_midblock_itemsizes"] = sorted({r.get("midblock_itemsize") for r in ires if r["ok"]})
|
|
summary["idat_chip_types"] = sorted({r.get("chip") for r in ires if r["ok"]})
|
|
|
|
# manifest / cluster file vs BeadArrayFiles
|
|
import module # type: ignore[import-not-found]
|
|
|
|
m = read_bpm(a.bpm)
|
|
b = module.BeadPoolManifest(str(a.bpm))
|
|
summary["bpm"] = {
|
|
"num_loci": m.num_loci,
|
|
"names": m.names == b.names,
|
|
"snps": m.snps == b.snps,
|
|
"chroms": m.chroms == b.chroms,
|
|
"map_infos": m.map_infos.tolist() == b.map_infos,
|
|
"address_a": m.address_a.tolist() == b.addresses,
|
|
"assay_types": m.assay_types.tolist() == b.assay_types,
|
|
"normalization_lookups": m.normalization_lookups().tolist() == b.normalization_lookups,
|
|
"n_bins": len(np.unique(m.norm_bin_ids())),
|
|
}
|
|
if not a.no_p2:
|
|
import multiprocessing as mp
|
|
import re
|
|
|
|
key_re = re.compile(r"(\d+_r\d{2}c\d{2})", re.IGNORECASE)
|
|
triples = []
|
|
for g in gtcs:
|
|
mk = key_re.search(Path(g).name)
|
|
k = mk.group(1).lower() if mk else Path(g).stem.lower()
|
|
if k in grn and k in red:
|
|
triples.append((g, str(grn[k]), str(red[k])))
|
|
summary["p2_matched_gtc_idat"] = len(triples)
|
|
with ProcessPoolExecutor(
|
|
a.workers, mp_context=mp.get_context("spawn"), initializer=_p2_init, initargs=(m.lite(),)
|
|
) as ex:
|
|
p2 = list(ex.map(check_raw_xy, triples, chunksize=4))
|
|
summary["p2_ok"] = sum(r["ok"] for r in p2)
|
|
summary["p2_total_diff_loci"] = sum(r.get("n_diff", 0) for r in p2)
|
|
summary["p2_swapped_loci"] = sum(r.get("swapped", 0) for r in p2)
|
|
summary["p2_ours_missing_vendor_nonzero"] = sum(r.get("ours_missing_vendor_nonzero", 0) for r in p2)
|
|
summary["p2_vendor_zero_ours_present"] = sum(r.get("vendor_zero_ours_present", 0) for r in p2)
|
|
summary["p2_failures"] = [r for r in p2 if not r["ok"]][:30]
|
|
e = read_egt(a.egt)
|
|
with open(a.egt, "rb") as fh:
|
|
be = module.ClusterFile.read_cluster_file(fh)
|
|
bad = 0
|
|
|
|
def same(a: float, b: float) -> bool:
|
|
return bool(np.float32(a) == np.float32(b) or (np.isnan(a) and np.isnan(b)))
|
|
|
|
for i, name in enumerate(e.names):
|
|
rec = be.get_record(name)
|
|
st = (rec.aa_cluster_stats, rec.ab_cluster_stats, rec.bb_cluster_stats)
|
|
if not all(
|
|
same(e.theta_mean[i, k], s.theta_mean)
|
|
and same(e.r_mean[i, k], s.r_mean)
|
|
and same(e.theta_dev[i, k], s.theta_dev)
|
|
and same(e.r_dev[i, k], s.r_dev)
|
|
and e.n[i, k] == s.N
|
|
for k, s in enumerate(st)
|
|
):
|
|
bad += 1
|
|
summary["egt"] = {
|
|
"num_records": e.num_records,
|
|
"dbv": e.data_block_version,
|
|
"extra_floats": e.extra_per_record,
|
|
"record_mismatches": bad,
|
|
}
|
|
if a.csv:
|
|
from simurg.formats.csv_manifest import compare_manifests, read_csv_manifest
|
|
|
|
summary["bpm_csv_problems"] = compare_manifests(m, read_csv_manifest(a.csv, load_sequences=False))
|
|
if gtcs:
|
|
g0 = __import__("simurg.formats.gtc", fromlist=["read_gtc"]).read_gtc(gtcs[0], check_write_complete=False)
|
|
summary["gtc_vs_bpm_num_snps"] = [g0.num_snps, m.num_loci]
|
|
summary["gtc_transforms_vs_bins"] = [len(g0.normalization_transforms), summary["bpm"]["n_bins"]]
|
|
|
|
summary["seconds"] = round(time.time() - t0, 1)
|
|
p2_passed = a.no_p2 or (
|
|
summary.get("p2_ok") == summary.get("p2_matched_gtc_idat", -1) and summary.get("p2_matched_gtc_idat", 0) > 0
|
|
)
|
|
passed = p2_passed and (
|
|
summary["gtc_ok"] == len(gtcs)
|
|
and summary["idat_ok"] == len(pairs)
|
|
and all(v for k, v in summary["bpm"].items() if isinstance(v, bool))
|
|
and summary["egt"]["record_mismatches"] == 0
|
|
and not summary.get("bpm_csv_problems")
|
|
)
|
|
summary["passed"] = passed
|
|
a.out.parent.mkdir(parents=True, exist_ok=True)
|
|
a.out.write_text(json.dumps(summary, indent=2, default=str) + "\n")
|
|
print(
|
|
json.dumps(
|
|
{
|
|
k: summary.get(k)
|
|
for k in (
|
|
"n_gtc",
|
|
"gtc_ok",
|
|
"gtc_roundtrip_identical",
|
|
"n_idat_pairs",
|
|
"idat_ok",
|
|
"p2_matched_gtc_idat",
|
|
"p2_ok",
|
|
"p2_total_diff_loci",
|
|
"passed",
|
|
"seconds",
|
|
)
|
|
}
|
|
)
|
|
)
|
|
return 0 if passed else 1
|
|
|
|
|
|
if __name__ == "__main__":
|
|
sys.exit(main())
|