Main genome retrieval function for an organism of interest.
By specifying the scientific name of an organism of interest the
corresponding fasta-file storing the genome of the organism of interest
can be downloaded and stored locally. Genome files can be retrieved from
several databases. In addition, the genome summary statistics for the
retrieved species is stored locally to provide users with
insights regarding the genome assembly quality (see summary_genome
for details).
This is useful when comparing genomes with large difference in genome assembly qualities.
getGenome(
db = "refseq",
organism,
reference = FALSE,
skip_bacteria = TRUE,
release = NULL,
gunzip = FALSE,
path = file.path("_ncbi_downloads", "genomes"),
assembly_type = "toplevel",
mute_citation = FALSE,
analyse_genome = FALSE
)
a character string specifying the database from which the genome shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
Organism selector id, there are three options to characterize an organism:
by scientific name
: e.g. organism = "Homo sapiens"
by database specific accession identifier
: e.g. organism = "GCF_000001405.37"
(= NCBI RefSeq identifier for Homo sapiens
)
by taxonomic identifier from NCBI Taxonomy
: e.g. organism = "9606"
(= taxid of Homo sapiens
)
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.
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.
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.
character, default location is paste0("set_", toupper(type))
a character, default "toplevel". id type of assembly, either "toplevel" or "primary_assembly" usually.
logical, default FALSE, indicating whether citation message should be muted.
logical, default FALSE. If TRUE, get general genome statistics like gc content etc. For more details, see ?summary_genome
File path to downloaded genome.
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 relative to file type, if you get fasta genomes it will be _ncbi_downloads/genomes'. In case the corresponding fasta file already exists within the '_ncbi_downloads/genomes' folder and is accessible within the workspace, no download process will be performed. For other file types the same rule applies.
Other getBio:
getBio()
,
getCDS()
,
getCollection()
,
getGFF()
,
getProteome()
,
getRNA()
Other genome:
getGenomeSet()
,
read_genome()