pysam.fetch and gene_id

[pkseq2017]

Hi there,

Does anyone know if/how pysam.fetch would accept gene_ids instead of ref+coordinate?


Thanks a lot for your help

[dpryan]

It won't accept that at all. You will need to convert that to a genomic range.

[pkseq2017]

Good to know, thank you!

So basically would be an extra layer of translating from some ref file to coordinates I guess?

[dpryan]

Exactly, you'd need to store the gene_id to position association somewhere.

[pkseq2017]

Alright! Thanks for your help