def write_block(data_block, plate_barcode, out_dir, snp_name_to_label, header, requested_sample_ids):
sample_id = adjust_immuno_sample_id(data_block.sample_id, plate_barcode)
if sample_id not in requested_sample_ids:
return sample_id, None
out_fn = os.path.join(out_dir, "%s.ssc" % sample_id)
header["sample_id"] = sample_id
stream = MessageStreamWriter(out_fn, PAYLOAD_MSG_TYPE, header)
for k in data_block.snp_names():
snp = data_block.snp[k]
snp_id = snp_name_to_label[snp["SNP Name"]]
call = "%s%s" % (snp["Allele1 - AB"], snp["Allele2 - AB"])
w_aa, w_ab, w_bb = WEIGHTS[call]
# GC Score = 0.0 ==> call = '--'
stream.write(
{
"sample_id": sample_id,
"snp_id": snp_id,
"call": getattr(SnpCall, call, SnpCall.NOCALL),
"confidence": float(snp["GC Score"]), # 1-gc_score? 1/gc_score?
"sig_A": float(snp["X Raw"]),
"sig_B": float(snp["Y Raw"]),
"w_AA": w_aa,
"w_AB": w_ab,
"w_BB": w_bb,
}
)
stream.close()
return sample_id, out_fn
def write_block(data_block, plate_barcode, out_dir, snp_name_to_label, header,
requested_sample_ids):
sample_id = adjust_immuno_sample_id(data_block.sample_id, plate_barcode)
if sample_id not in requested_sample_ids:
return sample_id, None
out_fn = os.path.join(out_dir, '%s.ssc' % sample_id)
header['sample_id'] = sample_id
stream = MessageStreamWriter(out_fn, PAYLOAD_MSG_TYPE, header)
for k in data_block.snp_names():
snp = data_block.snp[k]
snp_id = snp_name_to_label[snp['SNP Name']]
call = '%s%s' % (snp['Allele1 - AB'], snp['Allele2 - AB'])
w_aa, w_ab, w_bb = WEIGHTS[call]
# GC Score = 0.0 ==> call = '--'
stream.write({
'sample_id': sample_id,
'snp_id': snp_id,
'call': getattr(SnpCall, call, SnpCall.NOCALL),
'confidence': float(snp['GC Score']), # 1-gc_score? 1/gc_score?
'sig_A': float(snp['X Raw']),
'sig_B': float(snp['Y Raw']),
'w_AA': w_aa,
'w_AB': w_ab,
'w_BB': w_bb,
})
stream.close()
return sample_id, out_fn
def make_fake_ssc(mset, sample_id, probs, conf, fn):
header = {'markers_set' : mset.label, 'sample_id': sample_id}
stream = MessageStreamWriter(fn, PAYLOAD_MSG_TYPE, header)
labels = mset.add_marker_info['label']
for l, p_AA, p_BB, c in it.izip(labels, probs[0], probs[1], conf):
p_AB = 1.0 - (p_AA + p_BB)
w_aa, w_ab, w_bb = p_AA, p_AB, p_BB
stream.write({
'sample_id': sample_id,
'snp_id': l,
'call': SnpCall.NOCALL, # we will not test this anyway
'confidence': float(c),
'sig_A': float(p_AA),
'sig_B': float(p_BB),
'w_AA': float(w_aa),
'w_AB': float(w_ab),
'w_BB': float(w_bb),
})
stream.close()
def make_data_object(sample_id, fname, ms):
payload_msg_type = 'core.gt.messages.SampleSnpCall'
header = {'device_id' : 'FAKE',
'sample_id' : sample_id,
'min_datetime' : datetime.now().isoformat(),
'max_datetime' : datetime.now().isoformat()}
stream = MessageStreamWriter(fname, payload_msg_type, header)
for m in ms.markers:
call, sig_A, sig_B, weight_AA, weight_AB, weight_BB = random.choice(
[(SnpCall.AA, 1.0, 0.0, 1.0, 0.0, 0.0),
(SnpCall.AB, 1.0, 1.0, 0.0, 1.0, 0.0),
(SnpCall.BB, 0.0, 1.0, 0.0, 0.0, 1.0)])
stream.write({
'sample_id' : sample_id,
'snp_id' : m.id,
'call' : call,
'confidence' : 0.0,
'sig_A' : sig_A,
'sig_B' : sig_B,
'weight_AA' : weight_AA,
'weight_AB' : weight_AB,
'weight_BB' : weight_BB})
stream.close()
def write_ssc_data_set_file(fname, found_markers,
device_id, sample_id,
min_datetime, max_datetime, data):
payload_msg_type = 'core.gt.messages.SampleSnpCall'
header = {'device_id' : device_id,
'sample_id' : sample_id,
'min_datetime' : '%s' % min_datetime,
'max_datetime' : '%s' % max_datetime}
stream = MessageStreamWriter(fname, payload_msg_type, header)
for d in data:
found_marker = found_markers[d['Marker Name']]
m = found_marker['kb_marker']
stream.write({
'sample_id' : sample_id,
'snp_id' : m.id,
'call' : canonize_call(m.mask, d['Call']),
'confidence' : d['Quality Value'],
'sig_A' : d['Allele X Rn']*d['Passive Ref'],
'sig_B' : d['Allele X Rn']*d['Passive Ref'],
'w_AA' : d['Allele X Rn'],
'w_AB' : 0.0,
'w_BB' : d['Allele X Rn']})
stream.close()
