R/getKingdomAssemblySummary.R
getKingdomAssemblySummary.Rd
Retrieval function of the assembly_summary.txt file from NCBI for all kingdoms. The assembly_summary.txt files store available species on NCBI.
getKingdomAssemblySummary(
db,
skip_bacteria = TRUE,
file = assemblies_info_path(db)
)
database name. E.g. refseq
or genbank
.
Due to its enormous dataset size (> 700MB as of July 2023),
the bacterial summary file will not be loaded by default anymore. If users
wish to gain insights for the bacterial kingdom they needs to actively specify skip_bacteria = FALSE
. When skip_bacteria = FALSE
is set then the
bacterial summary file will be downloaded.
path, local path to total summary file, default is in tmp folder.
if (FALSE) {
# This example will run the default version of this function
# whereby information for Bacteria are not downloaded
test <- getKingdomAssemblySummary(db = "genbank", skip_bacteria = TRUE)
test
# Users can then retrieve information for Bacteria by skip_bacteria = FALSE
test2 <- getKingdomAssemblySummary(db = "genbank", skip_bacteria = FALSE)
test2
}