def test_read_sumstats():
x = ps.sumstats(
os.path.join(DIR, 'parse_test/test.sumstats'), dropna=True, alleles=True)
assert_equal(len(x), 1)
assert_array_equal(x.SNP, 'rs1')
assert_raises(ValueError, ps.sumstats, os.path.join(
DIR, 'parse_test/test.l2.ldscore.gz'))
def _read_sumstats(args, log, fh, alleles=False, dropna=False):
'''Parse summary statistics.'''
log.log('Reading summary statistics from {S} ...'.format(S=fh))
sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna)
log_msg = 'Read summary statistics for {N} SNPs.'
log.log(log_msg.format(N=len(sumstats)))
m = len(sumstats)
sumstats = sumstats.drop_duplicates(subset='SNP')
if m > len(sumstats):
log.log(
'Dropped {M} SNPs with duplicated rs numbers.'.format(M=m - len(sumstats)))
return sumstats