I'm using the Ensembl Perl API provided by Ensembl in order to collect informations about a set of genes (ENST IDs), all the transcripts from those genes (ENSG IDs), and all the variants from those transcripts (rs/cos/... IDs).
I'm actually looking for an efficient way to get the proteic sequences translated from each transcript variant (variations included), ie one proteic sequence per transcript variation.
Being unable to directly get the whole proteic sequence neither the nucleotidic sequence of a transcript variation in order to translate it (maybe I missed something), I had the idea of using a Slice object between the start and end positions of each transcript then translate the returned sequences based on the location and type of each transcript variation. But I realized it was tedious to handle frameshift variants and some variation cases.
That's the reason why I'm looking for a more direct and efficient way to get those proteic sequences.
If someone has the answer or any suggestion, I would greatly appreciate it.