download_run: Run download stage

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

Run download stage

Description

Run the second stage of phylotaR, download. This stage downloads sequences for all nodes with sequence numbers less than mxsqs. It hierarchically traverses the taxonomy for each node and downloads direct and subtree sequences for all descendants.

Usage

download_run(wd)

Arguments

wd	Working directory

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)

## End(Not run)

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