print('Time to encode all data: {} sec'.format(t.secs)) ################################### SINGLE META STAGE ############################## elif args.mode == 'single-meta': #ARG_CHECKER.check(args,mode='single-meta') mapper = Mapper() mapper.genotype_names = args.study_name mapper.chunk_size = MAPPER_CHUNK_SIZE mapper.reference_name = args.ref_name mapper.load_flip(args.mapper) mapper.load(args.mapper) mapper.cluster = args.cluster mapper.node = args.node phen = Reader('phenotype') phen.start(args.phenotype[0]) cov = Reader('covariates') cov.start(args.covariates) if cov.folder.n_files > 1: raise ValueError('In covariates folder should be only one file!') gen = Reader('genotype') gen.start(args.genotype[0], hdf5=args.hdf5, study_name=args.study_name[0], ID=False)
hdf5_iter=0 h5_name=args.save_name pytable_filter=tables.Filters(complevel=9, complib='zlib') gen=[] for i,j in enumerate(args.genotype): gen.append(Reader('genotype')) gen[i].start(j,hdf5=True, study_name=args.study_name[i], ID=False) RSID=[] 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)