Go from genbank accession numbers to taxonomic data in the NCBI database

gb_acc_to_taxonomy.R

# Go from genbank accession numbers to taxonomic data from the NCBI database

# `accs` is a (long) list of genbank accession numbers
# can only search max ca. 200 at a time because of NCBI limits
gb_acc <- rentrez::entrez_search(db = "nuccore", term = paste(accs[1:200], collapse = "|"), use_history = TRUE, retmax=200)

# For each accession, link to the taxonomy database
gb_tax_links <- rentrez::entrez_link(dbfrom = "nuccore",  db = "taxonomy", id = gb_acc$ids)

# Query the taxonomy database using the IDs in the links. Output is XML
tax_results_xml <- rentrez::entrez_fetch(db="taxonomy", id = gb_tax_links$links$nuccore_taxonomy, rettype="xml", retmode = "text")

# Convert the XML to a list for (somewhat) easier downstream processing
tax_results_list <-
tax_results_xml %>%
  stringr::str_split("\\n") %>%
  magrittr::extract2(1) %>%
  XML::xmlToList()