def postannotate_assays(assay_list, dbh, log, scanning_parameter, comm):
success = failed = skipped = subtotal = 0
total = len(assay_list)
start_time = time()
for (assay_id, sample_code) in assay_list:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.binned:
assay.postannotate( scanning_parameter )
success += 1
else:
skipped += 1
except RuntimeError as err:
log.append('ERR postannotating -- assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) )
)
failed += 1
subtotal += 1
if comm and subtotal % 5 == 0:
comm.cout = (
'postannotated: %d | failed: %d | skipped: %d | remaining: %d | estimated: %s'
% (success, failed, skipped, total-subtotal,
estimate_time(start_time, time(), success, total-subtotal )) )
if comm:
comm.cout = 'postannotated: %d | failed: %d | skipped: %d' % (
success, failed, skipped)
return (success, failed, skipped)
def align_assays(assay_list, dbh, log, scanning_parameter, comm):
success = failed = skipped = subtotal = 0
total = len(assay_list)
start_time = time()
for (assay_id, sample_code) in assay_list:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.preannotated:
retval = assay.alignladder(excluded_peaks = None)
(dpscore, rss, peaks_no, ladders_no, qcscore, remarks, method) = retval
if qcscore < 0.9:
log.append('WARN alignladder - '
'low qcscore %3.2f %4.2f %5.2f %d/%d %s for %s | %s'
% ( qcscore, dpscore, rss, peaks_no, ladders_no,
method, sample_code, assay.filename) )
success += 1
else:
skipped += 1
except RuntimeError as err:
log.append('ERR aligning ladder - assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) ) )
failed += 1
subtotal += 1
if comm and subtotal % 5 == 0:
comm.cout = (
'aligned: %d | failed: %d | skipped: %d | remaining: %d | estimated: %s'
% ( success, failed, skipped, total-subtotal,
estimate_time(start_time, time(), success, total-subtotal)) )
if comm:
comm.cout = 'aligned: %d | failed: %d | skipped: %d' % (
success, failed, skipped)
return (success, failed, skipped)
def process_assays(batch_id, login, comm = None, stage = 'all'):
dbh = get_dbhandler()
# get assay list
assay_list = get_assay_ids( batch_id )
log = []
stats = {}
scanning_parameter = params.Params()
failed = scanned = preannotated = aligned = called = binned = postannotated = subtotal = 0
total = len(assay_list)
start_time = time()
for (assay_id, sample_code) in assay_list:
subtotal += 1
if comm:
comm.cout = (
'failed: %d | scanned: %d | pre-annotated: %d | aligned: %d | '
'called: %d | binned: %d | post-annotated: %d | remaining: %d | estimated: %s' %
( subtotal - 1 - scanned,
scanned - preannotated,
preannotated - aligned,
aligned - called,
called - binned,
binned - postannotated,
postannotated,
total - subtotal - 1,
estimate_time(start_time, time(), subtotal - 1, total - subtotal - 1))
)
if stage in ['all', 'scan']:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.assigned:
assay.scan( scanning_parameter )
scanned += 1
except RuntimeError as err:
log.append('ERR scanning -- assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) ))
continue
except ZeroDivisionError as err:
log.append('ERR scanning -- FSA %s | %s - error division by zero' %
( assay.filename, sample_code))
continue
if stage in ['all', 'preannotate']:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.scanned:
assay.preannotate( scanning_parameter )
preannotated += 1
except RuntimeError as err:
log.append('ERR preannotating -- assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) ))
continue
if stage in ['all', 'align']:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.preannotated:
retval = assay.alignladder(excluded_peaks = None)
(dpscore, rss, peaks_no, ladders_no, qcscore, remarks, method) = retval
if qcscore < 0.9:
log.append('WARN alignladder - '
'low qcscore %3.2f %4.2f %5.2f %d/%d %s for %s | %s'
% ( qcscore, dpscore, rss, peaks_no, ladders_no,
method, sample_code, assay.filename) )
aligned += 1
except RuntimeError as err:
log.append('ERR aligning ladder - assay %s | %s - error: %s' %
(assay.filename, sample_code, str(err) ) )
continue
if stage in ['all', 'call']:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.aligned:
assay.call( scanning_parameter )
called += 1
except RuntimeError as err:
log.append('ERR calling -- assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) ))
continue
if stage in ['all', 'bin']:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.called:
assay.bin( scanning_parameter )
binned += 1
except RuntimeError as err:
log.append('ERR binning -- assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) ))
continue
if stage in ['all', 'postannotate']:
try:
with transaction.manager:
assay = dbh.get_assay_by_id(assay_id)
if assay.status == assaystatus.binned:
assay.postannotate( scanning_parameter )
postannotated += 1
except RuntimeError as err:
log.append('ERR postannotating -- assay %s | %s - error: %s' %
( assay.filename, sample_code, str(err) ))
continue
stats = {
'failed': subtotal - scanned,
'scanned': scanned - preannotated,
'preannotated': preannotated - aligned,
'aligned': aligned - called,
'called': called - binned,
'binned': binned - postannotated,
'postannotated': postannotated
}
if comm:
comm.cout = (
'failed: %d | scanned: %d | pre-annotated: %d | aligned: %d | '
'called: %d | binned: %d | post-annotated: %d' %
( stats['failed'],
stats['scanned'],
stats['preannotated'],
stats['aligned'],
stats['called'],
stats['binned'],
stats['postannotated'],
)
)
return stats, log