biomartr (version 0.5.1)

meta.retrieval.all: Perform Meta-Genome Retieval of all organisms in all kingdoms of life

Description

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")

Arguments

db

a character string specifying the database from which the genome shall be retrieved: db = "refseq", db = "genbank", db = "emsembl" or 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).

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.

Examples

## Not run: ------------------------------------
# # 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")
## ---------------------------------------------