clusters2_run: Run the cluster2 stage

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

Run the cluster2 stage

Description

Run the fourth stage of the phylotaR pipeline, cluster2. Identify clusters at higher taxonomic levels by merging sister clusters.

Usage

clusters2_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, clusters_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)
  clusters2_run(wd = wd)

## End(Not run)

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