elif args.mode == 'meta-stage':
#ARG_CHECKER.check(args,mode='meta-stage')
##### Init data readers #####
if args.derivatives is None:
raise ValueError(
'For meta-stage analysis partial derivatives data are required!'
)
mapper = Mapper()
mapper.chunk_size = MAPPER_CHUNK_SIZE
mapper.genotype_names = args.study_name
mapper.reference_name = args.ref_name # Reference dataset
if args.snp_id_inc is not None: # If this is not none the argument contains a table of snps to include
mapper.include = pd.DataFrame.from_csv(args.snp_id_inc,
index_col=None)
print 'Include:'
print mapper.include.head()
if 'ID' not in mapper.include.columns and (
'CHR' not in mapper.include.columns
or 'bp' not in mapper.include.columns):
raise ValueError(
'{} table does not have ID or CHR,bp columns'.format(
args.snp_id_inc))
if args.snp_id_exc is not None: # If this is not None the argument contains a table of snps to exclude
mapper.exclude = pd.DataFrame.from_csv(args.snp_id_exc,
index_col=None)
print 'Exclude:'
print mapper.exclude.head()
if 'ID' not in mapper.exclude.columns and (
'CHR' not in mapper.exclude.columns
if (cov.folder.n_files>1 and cov.folder.format!='.npy') or (cov.folder.n_files>2 and cov.folder.format=='.npy'): #TODO (middle) test
raise ValueError('In covariates folder should be only one file!')
gen=[]
for i,j in enumerate(args.genotype):
gen.append(Reader('genotype'))
gen[i].start(j,hdf5=args.hdf5, study_name=args.study_name[i], ID=False)
if args.mapper is not None:
mapper=Mapper()
mapper.chunk_size=MAPPER_CHUNK_SIZE
mapper.genotype_names=args.study_name
mapper.reference_name=args.ref_name
if args.snp_id_inc is not None:
mapper.include=pd.DataFrame.from_csv(args.snp_id_inc,index_col=None)
print 'Include:'
print mapper.include.head()
if 'ID' not in mapper.include.columns and ('CHR' not in mapper.include.columns or 'bp' not in mapper.include.columns):
raise ValueError('{} table does not have ID or CHR,bp columns'.format(args.snp_id_inc))
if args.snp_id_exc is not None:
mapper.exclude=pd.DataFrame.from_csv(args.snp_id_exc,index_col=None)
print 'Exclude:'
print mapper.exclude.head()
if 'ID' not in mapper.exclude.columns and ('CHR' not in mapper.exclude.columns or 'bp' not in mapper.exclude.columns):
raise ValueError('{} table does not have ID or CHR,bp columns'.format(args.snp_id_exc))
mapper.load(args.mapper)
mapper.load_flip(args.mapper)
mapper.cluster=args.cluster
mapper.node=args.node
else:
