Get taxID for NCBI AC, as well as tax path

get_taxid_from_ac.R

library(rentrez)
library(taxize)
library(XML)

get_docsum_val <- function(top, val) {
  sapply(getNodeSet(top,sprintf("/eSummaryResult/DocSum/Item[@Name='%s']", val)), xmlValue)
}

list_docsum_items <- function(top) {
  sapply(getNodeSet(top,"/eSummaryResult/DocSum/Item"), xmlGetAttr, name = "Name")
}

fetch_docsum_xml_root <- function(ac) {
  docsum <- entrez_fetch("nucleotide", ac, rettype = "docsum", retmode = "xml")  
  doc <- xmlTreeParse(docsum)
  xmlRoot(doc)
}

get_taxid_for_ac <- function(ac) {
  top <- fetch_docsum_xml_root(ac)
  get_docsum_val(top, "TaxId")
}

top <- fetch_docsum_xml_root("NC_000883")
taxid <- get_docsum_val(top, "TaxId")
list_docsum_items(top)

tax_path <- taxize::classification(taxid, db='ncbi')

Species_name <- sapply(tax_path, function(x) x$name[x$rank == "species"] )
Species_taxid <- sapply(tax_path, function(x) x$id[x$rank == "species"] )