Description Usage Arguments Value Examples
View source: R/retrieve_NCBI_taxonomy.R
This script downloads the full NCBI taxonomy from <ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz> and extracts it to the folder in 'target.dir'.
1 2 3 4 5 6 7 8 9 |
target.dir |
path to the folder where the files will be saved ( accepts relative and absolute paths) |
keep.all |
logical: should all files be kept (default) or only the ones used by _TaxonSampling_ ('nodes.dmp' and 'names.dmp')? |
method |
Method to be used for downloading files. Current download
methods are "internal", "wininet" (Windows only) "libcurl", "wget" and
"curl", and there is a value "auto": see _Details_ and _Note_ in the
documentation of |
unzip |
The unzip method to be used. See the documentation of
|
url |
URL of the full NCBI taxonomy file. |
timeout |
maximum time allowed for the download, in seconds. Increase when under a slow connection. |
... |
additional attributes (currently ignored) |
No return value, called for side effects (see Description).
1 2 3 4 | ## Not run:
TaxonSampling::retrieve_NCBI_taxonomy(target.dir = "data_files/taxdump")
## End(Not run)
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