List All Available Genomes either by kingdom, group, or subgroup — listGenomes • biomartr
Description: This function retrieves the names of all genomes available on the NCBI ftp:// server and stores the results in a file named 'overview.txt' inside the directory _ncbi_downloads' that is built inside the workspace.

# List All Available Genomes either by kingdom, group, or subgroup

Source: `R/listGenomes.R`
`listGenomes.Rd`

This function retrieves the names of all genomes available on the NCBI ftp:// server and stores the results in a file named 'overview.txt' inside the directory _ncbi_downloads' that is built inside the workspace.

    listGenomes(
      db = "refseq",
      type = "all",
      subset = NULL,
      details = FALSE,
      skip_bacteria = FALSE
    )

## Arguments

db

  a character string specifying the database for which genome availability shall be checked. Available options are:

  - `db = "refseq"`

  - `db = "genbank"`

  - `db = "ensembl"`

type

  a character string specifying a potential filter of available genomes. Available options are:

  - `type = "all"`

  - `type = "kingdom"`

  - `type = "group"`

  - `type = "subgroup"`

subset

  a character string or character vector specifying a subset of `type`. E.g. if users are interested in retrieving all `Eukaryota` species, they can specify: `type = "kingdom"` and `subset = "Eukaryota"`.

details

  a boolean value specifying whether only the scientific names of stored genomes shall be returned (details = FALSE) or all information such as

  - `organism_name`

  - `kingdoms`

  - `group`

  - `subgroup`

  - `file_size_MB`, etc.

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.

## Details

Internally this function loads the the overview.txt file from NCBI and creates a directory '_ncbi_downloads' in the `temdir()` folder to store the overview.txt file for future processing. In case the overview.txt file already exists within the '_ncbi_downloads' folder and is accessible within the workspace, no download process will be performed again.

## Note

Please note that the ftp:// connection relies on the NCBI or ENSEMBL server and cannot be accurately accessed via a proxy.

## Author

Hajk-Georg Drost

## Examples

    if (FALSE) {
    # print details for refseq
    listGenomes(db = "refseq")
    # print details for all plants in refseq
    listGenomes(db = "refseq", type = "kingdom")
    # print details for all plant groups in refseq
    listGenomes(db = "refseq", type = "group")
    # print details for all plant subgroups in refseq
    listGenomes(db = "refseq", type = "subgroup")
    # Ensembl
    listGenomes(db = "ensembl", type = "kingdom", subset = "EnsemblVertebrates")
    }