logger.info('Retrieved %d OMNIEXPRESS related plates' % len(plates))
logger.info('Calculating dependency tree')
kb.update_dependency_tree()
logger.info('Dependency tree loaded')
with open(args.ofile, 'w') as ofile:
writer = csv.DictWriter(ofile, ['source', 'study', 'label'],
delimiter='\t')
writer.writeheader()
inds = []
oe_index = get_first_index(kb, logger)
for pl in plates:
wells = list(kb.get_wells_by_plate(pl))
logger.info('Loaded %d wells for plate %s' %
(len(wells), pl.barcode))
for w in wells:
inds.append(kb.dt.get_connected(w, kb.Individual)[0])
inds = set(inds)
for ind in inds:
writer.writerow({
'source': ind.id,
'study': 'OMNIEXPRESS',
'label': OE_STCODE_PATTERN % oe_index
})
oe_index += 1
logger.info('Job completed')
logger.info('Retrieved %d OMNIEXPRESS related plates' % len(plates))
logger.info('Calculating dependency tree')
kb.update_dependency_tree()
logger.info('Dependency tree loaded')
with open(args.ofile, 'w') as ofile:
writer = csv.DictWriter(ofile, ['source', 'study', 'label'],
delimiter = '\t')
writer.writeheader()
inds = []
oe_index = get_first_index(kb, logger)
for pl in plates:
wells = list(kb.get_wells_by_plate(pl))
logger.info('Loaded %d wells for plate %s' % (len(wells),
pl.barcode))
for w in wells:
inds.append(kb.dt.get_connected(w, kb.Individual)[0])
inds = set(inds)
for ind in inds:
writer.writerow({'source' : ind.id,
'study' : 'OMNIEXPRESS',
'label' : OE_STCODE_PATTERN % oe_index})
oe_index += 1
logger.info('Job completed')
if __name__ == '__main__':
main(sys.argv[1:])
