About snap2anndata

[nigred]

Hello. I attempted to run snap2anndata following the tutorial (SnapATAC_to_anndata_March26th2020.ipynb) using sample data (atac_v1_adult_brain_fresh_5k.snap.rds). However, I received the error message below. How should I convert snap object to anndata object? I'm using python 3.7.1

Thank you for your help.

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During startup - Warning messages:
1: Setting LC_COLLATE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
5: Setting LC_PAPER failed, using "C"
6: Setting LC_MEASUREMENT failed, using "C"
UserWarning:convert_to_anndata_2.py:111:
featurepartially excluded from the conversion.
GRanges are not currently fully transfered into the Anndata.

UserWarning:convert_to_anndata_2.py:111:
peakpartially excluded from the conversion.
GRanges are not currently fully transfered into the Anndata.

Traceback (most recent call last):
File "convert_to_anndata_2.py", line 332, in
save='/home/ubuntu/result_dir/scATAC_Seq/snapATAC/200514_project/test/atac_v1_adult_brain_fresh_5k.snap.h5ad')
File "convert_to_anndata_2.py", line 309, in snap2anndata
copy=True))
File "convert_to_anndata_2.py", line 185, in make_Anndata
if (extra in input_data.keys()) and (extra not in adata.obs.columns) and (len(input_data[extra][1].tolist()) == len(adata.obs_names.tolist())):
AttributeError: 'StrVector' object has no attribute 'tolist'