) check_converter(args.out, args.study_name[0]) print('Time to convert all data: {} sec'.format(t.secs)) ################################### ENCODING ############################## elif args.mode == 'encoding': #ARG_CHECKER.check(args,mode='encoding') 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) phen = Reader('phenotype') phen.start(args.phenotype[0]) gen = Reader('genotype') gen.start(args.genotype[0], hdf5=args.hdf5, study_name=args.study_name[0], ID=False) e = Encoder(args.out) e.study_name = args.study_name[0] row_index, ids = study_indexes(phenotype=phen.folder._data, genotype=gen.folder._data)
parser.add_argument("-o", "--out", type=str, required=True, help="path to save result folder") parser.add_argument("-save_name", type=str, required=True, help="merge study name") parser.add_argument('-study_name', type=str, required=True,nargs='+', help=' Name for saved genotype data, without ext') parser.add_argument('-cluster', type=str, default='n', choices=['y','n'], help=' Is it parallel cluster job, default no') parser.add_argument('-node', nargs='+',help='number of nodes / this node number, example: 10 2 ') parser.add_argument('-split',type=int,help='Split size for merge genotypes') args = parser.parse_args() print args if __name__ == '__main__': mapper=Mapper(args.mapper_name) mapper.load(args.mapper) mapper.chunk_size=args.split 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())