def print_subsets(cls, outfilename, snpsubsets, names, add_other=False):
def snp_info_df(d):
bfile = d.genotypes_bedfile.filename
return pd.read_csv(bfile + '.bim',
delim_whitespace=True,
usecols=[0,1,2,3],
names=['CHR','SNP','CM','BP'])
# check that all snpsubsets have the same data set
if len(set([ss.dataset for ss in snpsubsets])) > 1:
print('error: all subsets must have the same underlying dataset')
return
if not outfilename.endswith('.gz'):
print('outfilename must end with ".gz". I only write zipped files')
return
# get snp info for this dataset
d = snpsubsets[0].dataset
df = snp_info_df(d)
# add the 'other' annotation if necessary
if add_other:
union = IntRangeSet()
for ss in snpsubsets:
union.update(ss.irs)
snpsubsets.append(SnpSubset(d, irs=d.all_snps() - union))
names.append('OTHER')
# create the pandas dataframe and output it
for name, ss in zip(names, snpsubsets):
df[name] = 0
df.ix[[i for i in ss.irs], name] = 1
df = df[['CHR','BP','SNP','CM'] + names]
with gzip.open(outfilename, 'wt') as write_file:
df.to_csv(write_file, index=False, sep='\t')
