| """Derive 2,504-unrelated membership per sample from INFO/AC_<SP>_unrel vs genotypes (derived, not a published list). |
| stdin: CHROM POS AC_AFR AC_AFR_unrel AC_EUR AC_EUR_unrel AC_EAS AC_EAS_unrel [GT...] (biallelic SNVs). |
| Constraint per (site, SP): AC_SP_unrel == sum over SP carriers of alt_count * [carrier unrelated]. |
| Propagation: a constraint with exactly one carrier of unknown status fixes it (value must be 0 or its count).""" |
| import sys, collections, json |
| ped = [l.split() for l in open(sys.argv[1])][1:] |
| samples = [l.strip() for l in open(sys.argv[2])] |
| sp_of = {r[1]: r[6] for r in ped}; pop_of = {r[1]: r[5] for r in ped} |
| SPS = ["AFR", "EUR", "EAS"] |
| idx_sp = [sp_of[s] for s in samples] |
| cons = []; bad = 0; sites = 0 |
| for line in sys.stdin: |
| p = line.rstrip("\n").split("\t"); sites += 1 |
| gts = p[8:] |
| car = collections.defaultdict(list) |
| for i, g in enumerate(gts): |
| n = g.count("1") |
| if n: car[idx_sp[i]].append((i, n)) |
| for k, sp in enumerate(SPS): |
| tot, unrel = int(p[2+2*k]), int(p[3+2*k]); c = car.get(sp, []) |
| if sum(n for _, n in c) != tot: bad += 1; continue |
| if c: cons.append((unrel, c)) |
| status = {} |
| evidence = collections.Counter(); conflicts = 0 |
| changed = True; rounds = 0 |
| while changed: |
| changed = False; rounds += 1 |
| for unrel, c in cons: |
| known = sum(n for i, n in c if status.get(i) == 1) |
| unk = [(i, n) for i, n in c if i not in status] |
| rem = unrel - known |
| if len(unk) == 1: |
| i, n = unk[0] |
| if rem == n: status[i] = 1; changed = True; evidence[i] += 1 |
| elif rem == 0: status[i] = 0; changed = True; evidence[i] += 1 |
| else: conflicts += 1 |
| elif not unk and rem != 0: conflicts += 1 |
| |
| viol = sum(1 for unrel, c in cons if all(i in status for i, _ in c) and sum(n for i, n in c if status[i] == 1) != unrel) |
| lab = {1: "unrel", 0: "related"} |
| res = {s: lab.get(status.get(i), "undetermined") for i, s in enumerate(samples)} |
| F = {r[1] for r in ped if r[2] == "0" and r[3] == "0"} |
| cnt = collections.Counter((sp_of[s], v) for s, v in res.items()) |
| pc = collections.Counter((pop_of[s], v, "founder" if s in F else "has_parent") for s, v in res.items() if pop_of[s] in ("YRI", "CEU", "CHB")) |
| print(json.dumps({"sites": sites, "constraints": len(cons), "ac_inconsistent": bad, "rounds": rounds, "conflicts_during_propagation": conflicts, |
| "violations_final": viol, "by_superpop": {f"{a}:{b}": v for (a, b), v in sorted(cnt.items())}, |
| "by_pop_and_pedigree": {f"{a}:{b}:{c}": v for (a, b, c), v in sorted(pc.items())}}, indent=1)) |
| with open(sys.argv[3], "w") as fh: |
| fh.write("SampleID\tPopulation\tSuperpopulation\tstatus\tpedigree_founder\n") |
| for s in samples: fh.write(f"{s}\t{pop_of[s]}\t{sp_of[s]}\t{res[s]}\t{int(s in F)}\n") |
|
|
