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:])