Perform Meta-Genome Retrieval of all organisms in all kingdoms of life — meta.retrieval.all • biomartr
Description: Download genomes, proteomes, cds, gff, rna, or assembly stats files of individual species of all kingdoms of life.

# Perform Meta-Genome Retrieval of all organisms in all kingdoms of life

Source: `R/meta.retrieval.all.R`
`meta.retrieval.all.Rd`

Download genomes, proteomes, cds, gff, rna, or assembly stats files of individual species of all kingdoms of life.

    meta.retrieval.all(db = "refseq", type = "genome", reference = FALSE)

## Arguments

db

  a character string specifying the database from which the genome shall be retrieved:

  - `db = "refseq"`

  - `db = "genbank"`

  - `db = "emsembl"`

  - `db = "ensemblgenomes"`

type

  type of sequences that shall be retrieved. Options are:

  - `type = "genome"` : for genome assembly retrieval; see also `getGenome`),

  - `type = "proteome"` : (for proteome retrieval; see also `getProteome`),

  - `type = "cds"` : (for coding sequence retrieval; see also `getCDS`),

  - `type = "gff"` : (for annotation file retrieval in gff format; see also `getGFF`),

  - `type = "gtf"` : (for annotation file retrieval in gtf format (only for ensembl and ensemblgenomes); see also `getGTF`),

  - `type = "rna"` : (for RNA file retrieval in fasta format; see also `getRNA`),

  - `type = "rm"` : (for Repeat Masker output file retrieval; see also `getRepeatMasker`),

  - `type = "assemblystats"` (for genome assembly quality stats file retrieval; see also `getAssemblyStats`).

reference

  a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome. Options are:

  - `reference = FALSE` (Default): all organisms (reference, representative, and non-representative genomes) are downloaded.

  - `reference = TRUE`: organisms that are downloaded must be either a reference or representative genome. Thus, most genomes which are usually non-reference genomes will not be downloaded.

## Value

a character vector storing the file paths of the retrieved files.

## Details

This function aims to perform bulk retrieval of all genomes of species for all kingdoms of life.

## See also

Other meta_retrival: `meta.retrieval()`

## Author

Hajk-Georg Drost

## Examples

    if (FALSE) {
    # download all genomes from refseq
    meta.retrieval.all(db = "refseq", type = "genome")
    # download all vertebrate genomes from genbank
    meta.retrieval.all(db = "genbank", type = "genome")
    # download all vertebrate genomes from ensemblgenomes
    meta.retrieval.all(db = "genbank", type = "ensemblgenomes")
    }