| |
| """E2 sample sets: the real-data sets with one fill individual replaced (approved 2026-11-02, option (a)). |
| |
| NA18498 (YRI, fill rank 54 of sets A and B) is not in the phase 3 call set. It is replaced, in the YRI fill only, |
| by NA18520, the next unused YRI individual in the frozen selection order (SELECTION.json order index 96). The |
| 32 view individuals of every set are unchanged; every other population's file is copied byte for byte. |
| The same sets are used for both call sets. |
| |
| Writes <bench>/real/e2_samples/{<POP>.tsv x 25, UNION_SAMPLES.txt, SWAP.json} (read-only); refuses to overwrite. |
| /usr/bin/python3 -B e2_make_samples.py |
| """ |
| import csv, hashlib, io, json, os, shutil, sys, time |
|
|
| B = "$WORK/bench_h2h_20260915" |
| SRC = f"{B}/real/autosomes_v1/samples" |
| OUT = f"{B}/real/e2_samples" |
| OLD, NEW, POP, RANK = "NA18498", "NA18520", "YRI", "54" |
|
|
|
|
| def sha(p): |
| return hashlib.sha256(open(p, "rb").read()).hexdigest() |
|
|
|
|
| def main(): |
| if os.path.exists(OUT): |
| sys.exit(f"refused: {OUT} exists") |
| sel = json.load(open(f"{SRC}/SELECTION.json")) |
| order = sel["populations"][POP]["order"] |
| used = set(sel["populations"][POP]["sets"]["A"]) | set(sel["populations"][POP]["sets"]["B"]) |
| nxt = [s for s in order if s not in used][0] |
| assert nxt == NEW and order.index(NEW) == 96, (nxt, order.index(NEW)) |
| os.makedirs(OUT) |
| pops = sorted(f[:-4] for f in os.listdir(SRC) if f.endswith(".tsv")) |
| assert len(pops) == 26 or len(pops) == 25, pops |
| files = {} |
| for pop in pops: |
| src, dst = f"{SRC}/{pop}.tsv", f"{OUT}/{pop}.tsv" |
| if pop != POP: |
| shutil.copyfile(src, dst) |
| else: |
| text = open(src, encoding="utf-8").read() |
| rows = list(csv.reader(io.StringIO(text), delimiter="\t")) |
| hdr = rows[0] |
| i_set, i_rank, i_role, i_id, i_ord = (hdr.index(k) for k in ("set", "rank", "role", "sample_id", "order_index")) |
| n = 0 |
| for r in rows[1:]: |
| if r[i_id] == OLD: |
| assert r[i_rank] == RANK and r[i_role] == "fill" and r[i_set] in ("A", "B"), r |
| r[i_id], r[i_ord] = NEW, str(order.index(NEW)) |
| n += 1 |
| assert n == 2, n |
| assert sum(r[i_id] == NEW for r in rows[1:]) == 2 |
| buf = io.StringIO() |
| csv.writer(buf, delimiter="\t", lineterminator="\n").writerows(rows) |
| open(dst, "w", encoding="utf-8").write(buf.getvalue()) |
| files[pop] = {"src_sha256": sha(src), "sha256": sha(dst), "changed": pop == POP} |
| old_union = open(f"{SRC}/UNION_SAMPLES.txt").read().split() |
| union = sorted({r["sample_id"] for pop in pops for r in csv.DictReader(open(f"{OUT}/{pop}.tsv"), delimiter="\t")}) |
| assert union == sorted((set(old_union) - {OLD}) | {NEW}), "union differs from old union - NA18498 + NA18520" |
| open(f"{OUT}/UNION_SAMPLES.txt", "w").write("\n".join(union) + "\n") |
| rec = {"schema": "paper_exp_20261102.e2.samples/1", "utc": time.strftime("%Y-%m-%dT%H:%M:%SZ", time.gmtime()), |
| "approval": "coordinator 2026-11-02: option (a) approved, NA18498 -> NA18520 in the YRI fill only, both call sets", |
| "reason": "NA18498 is not in the phase 3 GRCh38 call set (2,548 samples); every view individual is present", |
| "swap": {"population": POP, "sets": ["A", "B"], "rank": int(RANK), "role": "fill", "removed": OLD, "added": NEW, |
| "added_order_index": order.index(NEW), "rule": "next unused individual in the frozen SELECTION.json order"}, |
| "views_unchanged": True, "source_dir": SRC, "files": files, |
| "union": {"n": len(union), "sha256": sha(f"{OUT}/UNION_SAMPLES.txt")}} |
| json.dump(rec, open(f"{OUT}/SWAP.json", "w"), indent=1) |
| for f in os.listdir(OUT): |
| os.chmod(f"{OUT}/{f}", 0o444) |
| print(json.dumps({"out": OUT, "n_union": len(union), "yri_sha256": files[POP]["sha256"]})) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
