reset: Reset a phylotaR pipeline run

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

Reset a phylotaR pipeline run

Description

Resets the pipeline to a specified stage.

Usage

reset(wd, stage, hard = FALSE)

Arguments

wd	Working directory
stage	Name of stage to which the pipeline will be reset
hard	T/F, delete all cached data?

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(), 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 taxise
  taxise_run(wd = wd)
  # reset back to taxise as if it has not been run
  reset(wd = 'aotus', stage = 'taxise')
  # run taxise again ....
  taxise_run(wd = wd)

## End(Not run)

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