I have a bunch of protein IDs and I want to fetch the corresponding coding sequences (CDSs) without loosing the protein ID. I have managed to download the corresponding CDSs, but unfortunately, CDSs IDs are very different from protein IDs in NCBI.
I have the following R code:
library(rentrez) Prot_ids <- c("XP_012370245.1","XP_004866438.1","XP_013359583.1") links <- entrez_link(dbfrom="protein", db="nuccore", id=Prot_ids, by_id = TRUE)
And then, I used this command to "match" protein IDs with CDS IDs:
lapply(links2, function(x) x$links$protein_nuccore_mrna) []  "820968283" []  "861491027" []  "918634580"
However, as you can see the argument 'by_id=TRUE' just make a list of three elink objects but now I have lost the protein IDs.
I would want something like:
Protein ID XP_012370245.1 XP_004866438.1 XP_013359583.1
CDS ID XM_004866381.2 XM_012514791.1 XM_013504129.1
Any suggestion is very welcome, thanks!!