R/search_syn_in_ncbi.R

In FranzKrah/rmycobank: Interface to mycobank.org

#' Searches for the synonym on GenBank
#' 
#' Searches first for the synonyms and then searches for the UID code of the synonym present on GenBank
#' 
#' @param taxon a \code{character} containing fungal species name
#' 
#' 
#' @details The function is a wraper function of syno_mycobank and syns_on_ncbi.
#' 
#' @return data.frame with UIDs for the synonyms on GenBank
#' 
#' @author Franz-Sebastian Krah
#' 
#' @examples
#' taxon <- "Friesia annosa"
#' search_syn_in_ncbi(taxon = taxon)

search_syn_in_ncbi <- function(taxon){
  require("foreach")
  if(any(grep("_", taxon))==TRUE) taxon <- gsub("_", " ", taxon)
  search_syn_in_ncbi_s <- function(taxon){
    message("... downloading synonyms from MycoBank ...")
    synonyms <- syno_mycobank(taxon = taxon)
    res <- lapply(synonyms, syns_on_ncbi)
    res <- do.call(rbind, res)
    return(res)
  }
  if (length(taxon)==1){
    res <- search_syn_in_ncbi_s(taxon)
  }
    if(length(taxon)>1){
      res <- foreach(i = seq_along(taxon)) %do% search_syn_in_ncbi_s(taxon[i])
    }
  names(res) <- taxon
  return(res)
}