File size: 2,893 Bytes
765c2b7 | 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 | """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 = {} # i -> 1 unrel / 0 related
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
# final consistency check over all constraints with every carrier determined
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")
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