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colomemaria / epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python
BSD 3-Clause "New" or "Revised" License
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About snap2anndata #83

Open nigred opened 3 years ago

nigred commented 3 years ago

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.

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'