Retrieving the corresponding Haplotype CDS from Ensembl

Question

[Joseph Hughes]

Given a Ensembl protein identifier and amino acid substitution such as ENSP00000242351:701Q>E,851T>I, how do I programmatically retrieve and download the coding sequence (CDS) with the largest observed count.

I need to do this for a batch of different proteins*haplotypes so would like to use the REST API.

Answer 1

[Emily]

This REST API endpoint gets the haplotypes per transcript. The protein haplotypes have the associated cds haplotypes stored as hexes, which you can link to the cds haplotypes.

[Joseph Hughes]

So would this be taking the hex for the ENSP00000242351:701Q>E,851T>I in 'protein_haplotypes' and finding it as 'other_hex' in the 'cds_haplotypes'?

[Emily]

yes, this would be it. Or you can go the other way, and get the other_hex from the protein_haplotype and find the cds_haplotype it's the main hex for.