taxise_run: Run taxise stage

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Run taxise stage

Description

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.

Usage

taxise_run(wd)

Arguments

wd	Working directory

Details

Objects will be cached.

See Also

Other run-public: ClstrArc-class, ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), setup()

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)

## End(Not run)

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.