PMBio/mudatasets

Error loading brain9k dataset

Closed this issue · 1 comments

I get an error loading the brain 9k datasets, all other datasets work fine.

mudatasets.load('brain9k_multiome')
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Input In [4], in <cell line: 2>()
      1 import os
----> 2 mudatasets.load('brain9k_multiome')

File ~/my-conda-envs/scverse-tutorial/lib/python3.10/site-packages/mudatasets/core.py:219, in load(dataset, data_dir, full, files, version, with_info, backed, chunk_size)
    217 custom_loader = getattr(dset, "load", None)
    218 if callable(custom_loader):
--> 219     mdata = dset.load(data_dir=data_dir)
    220 else:
    221     warn("There seems to be no file with accepted extension to load (h5mu, h5ad, h5). There is no custom loader either.")

File ~/my-conda-envs/scverse-tutorial/lib/python3.10/site-packages/mudatasets/datasets/brain9k_multiome.py:150, in Brain9kMultiome.load(self, data_dir)
    148 counts = {"rna": "GSE162170_multiome_rna_counts.tsv.gz", "atac": "GSE162170_multiome_atac_counts.tsv.gz"}
    149 for m, fname in counts.items():
--> 150     fpath = os.path.join(data_dir, fname)
    151     modalities[m] = read_counts(fpath, sep="\t", obs_in_rows=False)
    153 mdata = MuData(modalities)

NameError: name 'os' is not defined

Importing os doesn't help.

gtca commented

Thanks for noticing. This datasets hasn't actually been made available as part of the v0.0.1 (though it was displayed in the list of datasets), now it's available in v0.0.2.