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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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protein_ids_at_locus() gives incorrect results #286

Open aeschriefer opened 1 year ago

aeschriefer commented 1 year ago

This line should be querying CDS, not transcript https://github.com/openvax/pyensembl/blob/1231e965e5a5c849e3242030742b6f6200b2de68/pyensembl/genome.py#L580

iskandr commented 4 months ago

I never thought to interpret it that way! If the UTR of a protein is affected by a mutation I still want to know the protein ID that is affected...but I guess that's up to individual preference? At the very least I guess the document should clearly specify the behavior.