Usually you want to use one of the specific set extractors
a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
a character vector storing the names of the organisms than shall be retrieved. There are three available options to characterize an organism:
the biological sequence type that shall be retrieved. Available options are
set_type = "genome"
set_type = "proteome"
set_type = "cds"
set_type = "gff"
set_type = "rna"
set_type = "collection"
(all the others)
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.
a numeric, the database release version of ENSEMBL (db = "ensembl"
). Default is release = NULL
meaning
that the most recent database version is used. release = 75
would for human would give the stable
GRCh37 release in ensembl. Value must be > 46, since ensembl did not structure their data
if the standard format before that.
a logical, indicating whether or not files should be unzipped.
logical, default FALSE. Updated backend cached files needed. Usually keep this false, to make ut run much faster. Only set to TRUE, if you believe you cache is outdated (Species only exist in newest release etc)
Due to its enormous dataset size (> 700MB as of July 2023),
the bacterial summary file will not be loaded by default anymore. If users
wish to gain insights for the bacterial kingdom they needs to actively specify skip_bacteria = FALSE
. When skip_bacteria = FALSE
is set then the
bacterial summary file will be downloaded.
character, default location is paste0("set_", toupper(set_type))
shall outlier lines be removed from the input annotation_file
?
If yes, then the initial annotation_file
will be overwritten and the removed outlier lines will be stored at tempdir
for further exploration.
a character, default "toplevel". id type of assembly, either "toplevel" or "primary_assembly" usually.
"gff3", alternative "gtf" for ensembl.
logical, default FALSE, indicating whether citation message should be muted.
File path to downloaded genomes (names are identifiers: 'new' (file was downloaded now), 'old' files did already exist)
Internally this function loads the the overview.txt file from NCBI:
refseq: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/
genbank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/
and creates a directory 'set_CDSs' to store the CDSs of interest as fasta files for future processing. In case the corresponding fasta file already exists within the 'set_CDSs' folder and is accessible within the workspace, no download process will be performed.
Other getBioSet:
getCDSSet()
,
getCollectionSet()
,
getGFFSet()
,
getGenomeSet()
,
getProteomeSet()
,
getRNASet()
if (FALSE) {
getBioSet("refseq", organisms = c("Arabidopsis thaliana",
"Arabidopsis lyrata",
"Capsella rubella"),
set_type = "cds")
}