biomartr (version 0.1.0)

meta.retrieval: Perform Meta-Genome Retieval

Description

Download genomes, proteomes, or CDS of all species within a kingdom of life.

Usage

meta.retrieval(kingdom, db = "refseq", type = "genome", out.folder = NULL)

Arguments

kingdom

a character string specifying the kingdom of the organisms of interest, e.g. "archaea","bacteria", "fungi", "invertebrate", "plant", "protozoa", "vertebrate_mammalian", or "vertebrate_other".

db

a character string specifying the database from which the genome shall be retrieved: refseq or genbank.

type

type of sequences that shall be retrieved. Either genome, proteome, or CDS.

out.folder

path to the folder in which downloaded genomes shall be stored. By default the kingdom name is used to name the output folder.

Details

This function aims to perform bulk retrieval of the genomes of species that belong to the same kingdom of life.

Examples

## Not run: 
# # get all available kingdoms
# getKingdoms()
# 
# # download all vertebrate genomes from refseq
# meta.retrieval(kingdom = "vertebrate_mammalian", db = "refseq", type = "genome")
# 
# # download all vertebrate genomes from genbank
# meta.retrieval(kingdom = "vertebrate_mammalian", db = "genbank", type = "genome")
# ## End(Not run)