R/meta.retrieval.all.R
meta.retrieval.all.RdDownload 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)a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "emsembl"
db = "ensemblgenomes"
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).
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.
a character vector storing the file paths of the retrieved files.
This function aims to perform bulk retrieval of all genomes of species for all kingdoms of life.
Other meta_retrival:
meta.retrieval()
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")
}