R/refseq_fromGene.R

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

#' @title Get the mRNA or protein accession
#'
#' @description \code{refseq_fromGene()} Returns the XP or XM accession from a single gene id. accession.
#'
#' @usage
#' refseq_fromGene(gene_symbol,sequence, retries)
#'
#' @param gene_symbol A character string of the gene symbol.
#' @param sequence A character string of the "XM" or "XP" to fetch data from mRNA or protein databases, respectively.
#' @param retries A numeric value to control the number of retry attempts to handle 502 errors.
#'
#' @returns A character vector containing the XP or XM id accessions corresponding to the especified `gene symbol`.
#'
#' @seealso \code{\link{refseq_XMfromXP}} to obtain the XM ids that encode a set of XP ids.
#' @seealso \code{\link{refseq_XPfromXM}} to obtain the XP ids encoded by a set of XM ids.
#'
#' @examples \donttest{
#' # Get the XM accessions from a set of gene ids
#' locs <- c("LOC101512347")
#' sapply(locs, function(x) refseq_fromGene (x, sequence = "XM", retries = 3), USE.NAMES = FALSE)
#'
#' # Get the XP accessions from a set of gene ids
#' locs <- c("LOC101512347")
#' sapply(locs, function(x) refseq_fromGene (x, sequence = "XP", retries = 3), USE.NAMES = FALSE)}
#'
#' @author Jose V. Die
#'
#' @export

refseq_fromGene <- function(gene_symbol , sequence = "XM", retries = 3) {

  ncbi = c()
  gene_id <- rentrez::entrez_search(db = "gene", term = gene_symbol)
  loc_links <- rentrez::entrez_link(dbfrom = "gene", id = gene_id$ids, db = "all")

  tryCatch({
    if (sequence == "XM") {

      if ("gene_nuccore" %in% names(loc_links$links)) {
        # if there is any mRNA ( = Gene type: protein coding)
        # the mRNA id is under the following link:
        mrna_id <- loc_links$links$gene_nuccore_refseqrna # extract just the mRNA

        # it may be > 1 mRNA
        for (i in 1:length(mrna_id)) {
          xm_summary <- rentrez::entrez_summary(db = "nuccore", id = mrna_id[i])
          ncbi <- c(ncbi, xm_summary$caption)
        }
      } else { # If there is not any mRNA (Gene type: pseudo)
        ncbi <- c(ncbi, "pseudo")
      }

    } else if (sequence == "XP") {
      if ("gene_protein_refseq" %in% names(loc_links$links))  {
        # the protein id is under the following link:
        p_id <- loc_links$links$gene_protein_refseq
        # It may be > 1 protein
        for (i in 1:length(p_id)) {
          xp_summary <- rentrez::entrez_summary(db = "protein", id = p_id[i])
          xp <- xp_summary$caption
          ncbi <- c(ncbi, xp)
        }
      } else { # if the link does not have any protein
        ncbi <- c(ncbi, "pseudo/no refseq 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_fromGene(gene_symbol, sequence, retries - 1))
      } else {
        stop(e)
      }
    }
  })
  return(ncbi)
}