R/annotate_with_NCBI_taxid.R

In currocam/taxa2hmmer: Get more out of homologous sequence search with HMMER

#' Retrieve the taxonomic data for a given NCBI taxon ID using a local database or as remote data sources.
#'
#' @param taxid A character or numeric vector containing the target NCBI taxon ID.
#' @param rank_vc A character vector containing the desired taxonomic ranks. If empty, all available taxonomic ranges will be retrieved.
#' @param mode A character vector, if "local" will use a local database instead of remote resources.  You will not have to download the database but it is slower.
#'
#' @return A DataFrame with columns `taxid` and taxonomic ranks.
#' @export
#' @examples
#' annotate_with_NCBI_taxid(7955, "species")
#' \dontrun{
#' taxa <- annotate_with_NCBI_taxid(
#'         taxid = hits$taxid,
#'         mode = "local")
#' }
annotate_with_NCBI_taxid <- function(taxid, rank_vc = NULL, mode = "remote") {
  if (!requireNamespace("taxizedb", quietly = TRUE) && mode == "local") {
    stop(
      "Package \"taxizedb\" must be installed to use this function with a local database.",
      call. = FALSE
    )
  }
  if (!requireNamespace("taxize", quietly = TRUE) && mode != "local") {
    stop(
      "Package \"taxize\" must be installed to use this function with remote data sources.",
      call. = FALSE
    )
  }
  taxid <- as.numeric(unique(taxid))
  ## Check arguments
  if(!is.character(rank_vc))
    rank_vc <- NULL
  if (mode != "local") {
    tax_cl <- taxize::classification(taxid, db = "ncbi") %>%
      purrr::discard(~ any(is.na(.x)))
  }
  if (mode == "local") {
    tax_cl <- taxizedb::classification(taxid) %>%
      purrr::discard(~ any(is.na(.x)))
  }
  tax_df <- purrr::map2_dfr(tax_cl, names(tax_cl), ~{
      .x$rank <- make.unique(.x$rank)
      .x %>%
      dplyr::select(name, rank) %>%
      dplyr::mutate("taxid" = as.character(.y))%>%
      tidyr::pivot_wider(names_from = rank,
                         values_from = name)
  }) %>%
    tibble::as_tibble()
  if(is.character(rank_vc)){
    tax_df <- tax_df %>%
      dplyr::select(unique(c(rank_vc, "taxid")))
  }
  return(tax_df)
}