print('Time to create fake phenotype is {}sec'.format(t_phen.secs))
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],
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())
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
