Ensemble version of transcript in python API?

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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Open arogozhnikov opened 3 years ago

arogozhnikov commented 3 years ago

Ensemble GTF file keeps versions of transcripts, is there way to get those for Transcript object?

iskandr commented 3 years ago

I think we strip it out when parsing the GTF, which I think got added to keep compat. with older GTFs that didn't have these versions.

It wouldn't be hard to keep the versions when present, I'll look into whether that can happen just in pyensembl or also requires changing gtfparse.

arogozhnikov commented 3 years ago

that would be nice. Particular usecases:

when aligning against transcriptome, counts and psuedoalignment are given for names with versions, so I can't for instance go from gene -> transcript -> reads and counts, some hacks are required

austinv11 commented 2 weeks ago

Has there been any update to this? I need to retain transcript ids and transcript versions when doing genome queries.