Download database

Download .seq.tar files from the latest GenBank release.

Usage

db_download(
  db = "nucleotide",
  overwrite = FALSE,
  preselection = NULL,
  max_tries = 1
)

Arguments

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).

Value

T/F, if all files download correctly, TRUE else FALSE.

Details

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!).

See also

ncbi_acc_get()

Other database: count_db_ids(), db_create(), db_delete(), demo_db_create(), is_in_db(), list_db_ids()

Examples

if (FALSE) {
library(restez)
restez_path_set(filepath = 'path/for/downloads')
db_download()
}