R/find_taxonomy.R

In compbiomed/animalcules: Interactive microbiome analysis toolkit

#' Find the taxonomy for unlimited tids
#'
#' @param tids Given taxonomy ids
#' @return A list of taxon levels with information
#'
#' @examples
#' taxonLevels <- find_taxonomy(tids = 1200)
#'
#' @import rentrez

#' @export
find_taxonomy <- function(tids) {
    if (is.null(tids)) {
        return(NULL)
    }
    if (length(tids) <= 300) {
        taxonLevels <- find_taxonomy_300(tids)
    } else {
        taxonLevels <- list()
        batch.num <- ceiling(length(tids) / 300)
        for (i in seq_len(batch.num)) {
            if (i == batch.num) {
                tids.batch <- tids[((i - 1) * 300 + 1):length(tids)]
            } else {
                tids.batch <- tids[((i - 1) * 300 + 1):(i * 300)]
            }
            taxonLevels <- c(taxonLevels, find_taxonomy_300(tids.batch))
        }
    }
    return(taxonLevels)
}