def next(self):
r = csv.DictReader.next(self)
try:
mask = split_mask(r['mask'].upper())
except ValueError, e:
print "ERROR: %r: %s, skipping" % (label, e)
return self.next()
def next(self):
r = csv.DictReader.next(self)
try:
mask = split_mask(r['mask'].upper())
except ValueError, e:
print "ERROR: %r: %s, skipping" % (label, e)
return self.next()
def check_mask(mask):
try:
lflank, alleles, rflank = split_mask(mask)
except ValueError:
problem = "bad mask format"
else:
if not(2 <= len(alleles) <= 4 and set(alleles) <= POSSIBLE_ALLELES):
problem = "bad alleles: %r" % list(alleles)
else:
problem = None
return problem
def build_fastq_records(label, mask, name_serializer, logger=None):
logger = logger or NullLogger()
records = []
try:
lflank, alleles, rflank = split_mask(mask)
except ValueError:
status = "no mask" if mask == "None" else "bad mask format"
logger.warn("%r: %s, skipping" % (label, status))
else:
snp_offset = len(lflank)
for a, c in izip(alleles, ALLELE_CODES):
seq = "%s%s%s" % (lflank, a, rflank)
seq_id = name_serializer.serialize(label, c, snp_offset, alleles)
r = ('@%s' % seq_id, seq, '+%s' % seq_id, '~'*len(seq))
records.append(r)
return records
def build_fastq_records(label, mask, name_serializer, logger=None):
logger = logger or NullLogger()
records = []
try:
lflank, alleles, rflank = split_mask(mask)
except ValueError:
status = "no mask" if mask == "None" else "bad mask format"
logger.warn("%r: %s, skipping" % (label, status))
else:
snp_offset = len(lflank)
for a, c in izip(alleles, ALLELE_CODES):
seq = "%s%s%s" % (lflank, a, rflank)
seq_id = name_serializer.serialize(label, c, snp_offset, alleles)
r = ('@%s' % seq_id, seq, '+%s' % seq_id, '~' * len(seq))
records.append(r)
return records
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))
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))
def test_good(self):
for s, t in SPLIT_MASK_PAIRS:
self.assertEqual(usnp.split_mask(s), t)
with open(fn) as f:
reader = csv.DictReader(f, delimiter="\t")
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,
