Run the first stage of phylotaR, taxise. This looks up all descendant taxonomic nodes for a given taxonomic ID. It then looks up relevant taxonomic information and generates a taxonomic dictionary for user interaction after phylotaR has completed.

taxise_run(wd)

Arguments

wd

Working directory

Details

Objects will be cached.

See also

Examples

# NOT RUN {

  # Note: this example requires BLAST and internet to run.

  # example with temp folder
  wd <- file.path(tempdir(), 'aotus')
  # setup for aotus, make sure aotus/ folder already exists
  if (!dir.exists(wd)) {
    dir.create(wd)
  }
  ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  # individually run stages
  taxise_run(wd = wd)
# }