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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.

Usage

listGenomes(
  db = "refseq",
  type = "all",
  subset = NULL,
  details = FALSE,
  update = 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", no subset

  • type = "kingdom", subset on kingdom

  • type = "group", subset on group

  • type = "subgroup", subset on 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.

update

logical, default FALSE. If TRUE, update cached list, if FALSE use existing cache (if it exists). For cache location see cachedir()

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) { # \dontrun{
# 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")
} # }