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.
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")
}