R/refseq_fromGene_action.R

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

#' @title Get the mRNA or protein accession
#'
#' @description \code{refseq_fromGene_action()} Returns the mRNA or protein accession from a single GeneID.
#'
#' @usage
#' refseq_fromGene_action(GeneID, sequence, retries)
#'
#' @param GeneID A character string of the GeneID.
#' @param sequence A character string of the mRNA or protein accession 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 mRNA or protein accession corresponding to the especified `GeneID`.
#'
#' @author Jose V. Die

refseq_fromGene_action <- function (GeneID, sequence = "transcript", retries = 4) { 
  
  ncbi = c()
  gene_id <- rentrez::entrez_search(db = "gene", term = GeneID)
  loc_links <- rentrez::entrez_link(dbfrom = "gene", id = gene_id$ids, 
                                    db = "all")
  
  
  tryCatch({
    
    if (sequence == "transcript") { 
      
      if ("gene_nuccore" %in% names(loc_links$links)) { 
        mrna_id <- loc_links$links$gene_nuccore_refseqrna
        if(is.null(mrna_id)) { 
          ncbi <- paste(paste0("NOTE: The GeneID=", GeneID), "is not listed with any transcript sequence in RefSeq")
        } else {
          for (i in 1:length(mrna_id)) {
            xm_summary <- rentrez::entrez_summary(db = "nuccore", 
                                                  id = mrna_id[i])
            if(is.null(xm_summary)) {
              ncbi <- c(ncbi, "no RefSeq transcript")
              
            } else {ncbi <- c(ncbi, xm_summary$caption) }
            
          }  
        }
        
      }
      
    }
    
    if (sequence == "protein") { 
      if ("gene_protein_refseq" %in% names(loc_links$links)) { 
        p_id <- loc_links$links$gene_protein_refseq
        if(is.null(p_id)) { 
          ncbi <- paste(paste0("NOTE: The GeneID=", GeneID), "is not listed with any protein sequence in RefSeq")
        } else {
          for (i in 1:length(p_id)) { 
            xp_summary <- rentrez::entrez_summary(db = "protein", 
                                                  id = p_id[i])
            
            if(is.null(xp_summary)) {
              ncbi <- c(ncbi, "no RefSeq protein") 
              
            } else {ncbi <- c(ncbi, xp_summary$caption) }
            
          }  
        }
        
      }
      
    }
    
  }, error = function(e){
    if (inherits(e, "error")) {
      if (grepl("HTTP error: 502", e$message) && retries > 0) {
        message("Retrying...\n")
        Sys.sleep(5)
        return(refseq_fromGene_action(GeneID, sequence, retries - 1))
      }
      else { stop(e) }
    }
  })
  return(ncbi)
}