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) # Load the mapper files
mapper.load_flip(args.mapper,
encode=args.encoded) # often args.encoded is is null
mapper.cluster = args.cluster # Is n by default
mapper.node = args.node
Analyser = HaseAnalyser()
pard = []
with Timer() as t:
for i, j in enumerate(args.derivatives):
pard.append(Reader('partial'))
pard[i].start(j, study_name=args.study_name[i])
pard[i].folder.load()
print "time to set PD is {}s".format(t.secs)
PD = [
False if isinstance(i.folder._data.b4, type(None)) else True
for i in pard
]
