Description Usage Arguments Details See Also Examples
Run the first stage of phylotaR, taxise. This looks up all descendant taxonomic nodes for a given taxonomic ID. It then looks up relevant taxonomic information and generates a taxonomic dictionary for user interaction after phylotaR has completed.
1 | taxise_run(wd)
|
wd |
Working directory |
Objects will be cached.
Other run-public: ClstrArc-class
,
ClstrRec-class
,
Phylota-class
, SeqArc-class
,
SeqRec-class
, TaxDict-class
,
TaxRec-class
, clusters2_run
,
clusters_run
,
parameters_reset
, reset
,
restart
, run
,
setup
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
## End(Not run)
|
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