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Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms

Source: 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.

Usage

getKingdomAssemblySummary(
  db,
  skip_bacteria = TRUE,
  file = assemblies_info_path(db)
)

Arguments

db

database name. E.g. refseq or genbank.

skip_bacteria

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.

file

path, local path to total summary file, default is in tmp folder.

See also

getSummaryFile, getMetaGenomeSummary, get.ensembl.info

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# 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
} # }