meta.retrieval.all: Perform Meta-Genome Retrieval of all organisms in all...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/meta.retrieval.all.R

Description

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

Usage

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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"

  • 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).

Details

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

Value

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

Author(s)

Hajk-Georg Drost

See Also

meta.retrieval

Examples

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## 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")

## End(Not run)

biomartr documentation built on July 2, 2018, 1:02 a.m.