View source: R/meta.retrieval.all.R
meta.retrieval.all | R Documentation |
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)
db |
a character string specifying the database from which the genome shall be retrieved:
|
type |
type of sequences that shall be retrieved. Options are:
|
reference |
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:
|
This function aims to perform bulk retrieval of all genomes of species for all kingdoms of life.
a character vector storing the file paths of the retrieved files.
Hajk-Georg Drost
Other meta_retrival:
meta.retrieval()
## 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)
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