Nothing
#' Update NCBI taxonomy database
#' @return none (updated files will be saved in PhyloProfile package folder)
#' @author Vinh Tran {tran@bio.uni-frankfurt.de}
updateNcbiTax <- function() {
# get latest NCBI taxonomy database and processing
message("1) Getting latest NCBI taxonomy database and processing...")
preProcessedTaxonomy <- processNcbiTaxonomy()
# save to preProcessedTaxonomy.txt file within PhyloProfile pkg folder
message("2) Saving new data into preProcessedTaxanomy.txt file...")
packgePath <- find.package("PhyloProfile")
write.table(
preProcessedTaxonomy,
file = paste0(packgePath,"/PhyloProfile/data/preProcessedTaxonomy.txt"),
col.names = TRUE,
row.names = FALSE,
quote = FALSE,
sep = "\t"
)
message("3) FINISHED! Your NCBI taxonomy database has been updated!<br>")
message("Now you can re-upload your input or restart PhyloProfile.")
}
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