scverse / genomic-features

Genomic Features in Python from BioConductor's AnnotationHub
https://genomic-features.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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`list_columns` includes columns from `"metadata"` and `"chromosome"` table #42

Closed ivirshup closed 2 months ago

ivirshup commented 1 year ago

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import genomic_features as gf

ensdb = gf.ensembl.annotation(species="Hsapiens", version="108")
ensdb.list_columns()
['seq_name',
 'seq_length',
 'is_circular',
...
 'name',
 'value',
...
]

I think we shouldn't include columns from these tables in the output of list_columns, since we can't join on them in the genes, transcripts, and exons functions. To me, this function tells you what possible values are for the cols argument, which I don't think these satisfy.

What do you think @lauradmartens?

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ivirshup commented 2 months ago

I thought I commented this somewhere, but list_columns can also return repeated column names. It would be good to fix that too.