Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms — getKingdomAssemblySummary • biomartr
Description: Retrieval function of the assembly_summary.txt file from NCBI for all kingdoms. The assembly_summary.txt files store available species on NCBI.

# 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.

    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) {
    # 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
    }