clusters_run: Run the cluster stage

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

Run the cluster stage

Description

Run the third stage of the phylotaR pipeline, cluster. This stage hierarchically traverses the taxonomy identifying all direct and subtree clusters from downloaded sequences. Any taxonomic nodes too small for cluster identification are placed into paraphyletic clusters.

Usage

clusters_run(wd)

Arguments

wd	Working directory

See Also

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

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)
  download_run(wd = wd)
  clusters_run(wd = wd)

## End(Not run)

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