Description Usage Arguments Examples
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.
1 | download_run(wd)
|
wd |
Working directory |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## 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)
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