R/refseq_AAlen_action.R

In jdieramon/refseqR: Common Computational Operations Working with RefSeq Entries (GenBank)

#' @title Get the amino acid length from a protein accession
#'
#' @description \code{refseq_AA_len_action()} Returns the amino acid length from a single protein accession.
#'
#' Depending on the function, available accessions in \code{refseqR} include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
#' 
#' @usage
#' refseq_AAlen_action(protein, retries)
#'
#' @param protein A character string of the protein id.
#' @param retries A numeric value to control the number of retry attempts to handle internet errors.
#'
#'
#' @returns A numeric value representing the aa length of the `protein`.
#'
#' @seealso \code{\link{refseq_RNA2protein}} to obtain the protein ids encoded by a set of transcript ids.
#'
#' @author Jose V. Die

refseq_AAlen_action <- function(protein, retries = 4) {
  tryCatch({
    # Get the item list for that protein id
    xpinfo <- rentrez::entrez_summary(db = "protein", id = protein)
  }, error = function(e){
    if (inherits(e, "error")) {
      if (grepl("HTTP error: 502", e$message) && retries > 0) {
        message("Retrying...\n")
        Sys.sleep(5)  # Wait for 5 seconds before retrying
        return(refseq_AAlen_action(protein, retries - 1))
      } else {
        stop(e)
      }
    }
  })
  # Get the protein length
  return(xpinfo$slen)
}