Closed le-ander closed 4 years ago
Hi Anna,
there seems to be a very small bug in build_mtx_fly():
I get:
loading the barcodes --------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-6-1ca708327c27> in <module> ----> 1 epi.ct.bld_mtx_fly(paths['rawdir']+'fragments.tsv.gz', paths['rawdir']+'fragments.tsv.gz.tbi', paths['writedir']+'../../data_other/atac_geneid_features.bed') ~/.local/lib/python3.7/site-packages/episcanpy/count_matrix/_bld_atac_mtx.py in bld_mtx_fly(tsv_file, tbi_file, annotation, csv_file, genome, DATADIR, save) 135 with gzip.open(tsv_file, 'rb') as f_in: 136 with open(tsv_file.rstrip('.gz'), 'wb') as f_out: --> 137 shutil.copyfileobj(f_in, f_out) 138 df = pd.read_csv(tsv_file.rstrip('.gz'), sep='\t', header=None) 139 barcodes = list(sorted(set(df.loc[:,3].tolist()))) NameError: name 'shutil' is not defined
I guess there is just an import statement missing
Hi Leander,
Thank you for reporting the bug. I just fixed it.
Hi Anna,
there seems to be a very small bug in build_mtx_fly():
I get:
I guess there is just an import statement missing