def canonize_call(mask, abi_call):
"""
Canonize call against top mask. Directly uses the base
called by TaqMan to compute the relevant allele code.
"""
if abi_call.upper() == 'BOTH':
return SnpCall.AB
if abi_call.upper() == 'UNDETERMINED':
return SnpCall.NOCALL
_, call_base = abi_call.split('-')
_, alleles, _ = split_mask(mask)
if call_base in [alleles[0], rc(alleles[0])]:
return SnpCall.AA
elif call_base in [alleles[1], rc(alleles[1])]:
return SnpCall.BB
else:
raise ValueError('Cannot map %s (alleles: %s)' % (abi_call, alleles))
writer = csv.DictWriter(outf,
delimiter="\t",
lineterminator=os.linesep,
fieldnames=fieldnames)
writer.writeheader()
for i, (m, r) in enumerate(it.izip(markers, records)):
assert m.id == r['source']
try:
_, stored_alleles, _ = snp.split_mask(m.mask)
except ValueError:
sys.stdout.write("WARNING: could not split mask for %r\n" %
r['source'])
flip = False
else:
alleles = r['allele_a'], r['allele_b']
fl_alleles = r['allele_b'], r['allele_a']
if alleles == stored_alleles or rc(alleles) == stored_alleles:
flip = False
elif fl_alleles == stored_alleles or rc(
fl_alleles) == stored_alleles:
flip = True
else:
raise ValueError("%s: got inconsistent mask from db: %r" %
(m.id, m.mask))
index = r.get("marker_indx", i)
writer.writerow({
"marker_vid": m.id,
"marker_indx": index,
"allele_flip": flip
})
records = [r for r in reader]
vids = [r['source'] for r in records]
markers = kb.get_snp_markers(vids=vids, col_names=['vid', 'mask'])
with open(outfn, 'w') as outf:
fieldnames = ['marker_vid', 'marker_indx', 'allele_flip']
writer = csv.DictWriter(outf, delimiter="\t", lineterminator=os.linesep,
fieldnames=fieldnames)
writer.writeheader()
for i, (m, r) in enumerate(it.izip(markers, records)):
assert m.id == r['source']
try:
_, stored_alleles, _ = snp.split_mask(m.mask)
except ValueError:
sys.stdout.write("WARNING: could not split mask for %r\n" % r['source'])
flip = False
else:
alleles = r['allele_a'], r['allele_b']
fl_alleles = r['allele_b'], r['allele_a']
if alleles == stored_alleles or rc(alleles) == stored_alleles:
flip = False
elif fl_alleles == stored_alleles or rc(fl_alleles) == stored_alleles:
flip = True
else:
raise ValueError("%s: got inconsistent mask from db: %r" %
(m.id, m.mask))
index = r.get("marker_indx", i)
writer.writerow({"marker_vid": m.id, "marker_indx": index,
"allele_flip": flip})
def build_index_key(seq): return min(seq, rc(seq))