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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.

Usage

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