Is there a python equivalent to ensembldb? I want to get genome coordinates for a transcript (like the function transcriptToGenome) but need to do it in python. I wrote a R script that I'm calling from python but I was hoping there was a more direct way to do this.



pyensembl should do the job:

>>> from pyensembl import EnsemblRelease
>>> data = EnsemblRelease(76)
>>> data.transcript_by_id("ENST00000506751")
Transcript(..., contig='5', start=140861224, end=140863521, strand='+', genome='GRCh38')
  • $\begingroup$ Thanks so much this is perfect. Do you happen to know if there is anything similar for NCBI? $\endgroup$
    – Greg
    Jul 12 at 15:07
  • $\begingroup$ Maybe biopython.org/docs/1.75/api/Bio.Entrez.html? $\endgroup$
    – haci
    Jul 12 at 16:16
  • $\begingroup$ I don't see a way to map coordinates with Bio.Entrez unfortunately. Thanks though. $\endgroup$
    – Greg
    Jul 12 at 19:29

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