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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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Bug report [BUG] about tutorial #186

Open Keep-Raining opened 1 week ago

Keep-Raining commented 1 week ago

Describe the bug /src/pycisTopic/gene_annotation.py, line 668 /src/pycisTopic/cli/subcommand/qc.py, line 212, 219: there is no parameter 'has_header', I think it should be 'include_header'.

and /src/pycisTopic/cli/subcommand/qc.py, line 498, the CB column is mistakenly named as 'by'.

To Reproduce Follow the tutorial https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html#QC: Cell17 and Cell24

https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html#QC: Cell24

ghuls commented 1 week ago

The Polars_1xx branch should have this fixes (and a lot of other Polars syntax updates: https://github.com/aertslab/pycisTopic/tree/polars_1xx

https://github.com/aertslab/pycisTopic/commit/9892252c0b364e9b16ff0c1d56dbc29fcdb65056 https://github.com/aertslab/pycisTopic/commit/ca9b230651c59b1cc4719cf42840554bbb733638

Tutorials still need to be updated.