SUB_ID=[] for i in gen: SUB_ID.append(i.folder._data.get_id()) mapper.cluster=args.cluster mapper.node=args.node while True: if args.cluster=='n': SNPs_index, keys=mapper.get_next() else: chunk=mapper.chunk_pop() if chunk is None: SNPs_index=None break print chunk SNPs_index, keys=mapper.get_chunk(chunk) if SNPs_index is None: break RSID.append(keys) data=merge_genotype(gen, SNPs_index) #TODO (high) add mapper print data.shape if args.cluster=='n': h5_gen_file = tables.openFile( os.path.join(args.out,str(hdf5_iter)+'_'+h5_name+'.h5'), 'w', title=args.save_name) else:#TODO (high) check! h5_gen_file = tables.openFile( os.path.join(args.out,str(chunk[0])+'_' +str(chunk[1])+'_'+h5_name+'.h5'), 'w', title=args.save_name) hdf5_iter+=1
