View source: R/db-setup-tools.R
db_download | R Documentation |
Download .seq.tar files from the latest GenBank release.
db_download(
db = "nucleotide",
overwrite = FALSE,
preselection = NULL,
max_tries = 1
)
db |
Database type, only 'nucleotide' currently available. |
overwrite |
T/F, overwrite pre-existing downloaded files? |
preselection |
Character vector of length 1; GenBank domains to download. If not specified (default), a menu will be provided for selection. To specify, provide either a single number or a single character string of numbers separated by spaces, e.g. "19 20" for 'Phage' (19) and 'Unannotated' (20). |
max_tries |
Numeric vector of length 1; maximum number of times to attempt downloading database (default 1). |
In default mode, the user interactively selects the parts (i.e., "domains")
of GenBank to download (e.g. primates, plants, bacteria ...). Alternatively,
the selected domains can be provided as a character string to preselection
.
The max_tries
argument is useful for large databases that may otherwise
fail due to periodic lapses in internet connectivity. This value can be set
to Inf
to continuously try until the database download succeeds (not
recommended if you do not have an internet connection!).
T/F, if all files download correctly, TRUE else FALSE.
ncbi_acc_get()
Other database:
count_db_ids()
,
db_create()
,
db_delete()
,
demo_db_create()
,
is_in_db()
,
list_db_ids()
## Not run:
library(restez)
restez_path_set(filepath = 'path/for/downloads')
db_download()
## End(Not run)
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