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Coding Sequence Retrieval

Source: R/getCDS.R
getCDS.Rd

Main retrieval function for coding sequences (CDS) of an organism of interest. By specifying the scientific name of an organism of interest the corresponding fasta-file storing the CDS information for the organism of interest can be downloaded and stored locally. CDS files can be retrieved from several databases.

Usage

getCDS(
  db = "refseq",
  organism,
  reference = FALSE,
  skip_bacteria = TRUE,
  release = NULL,
  gunzip = FALSE,
  path = file.path("_ncbi_downloads", "CDS"),
  mute_citation = FALSE
)

Arguments

db

a character string specifying the database from which the genome shall be retrieved:

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

organism

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)

reference

a logical value indicating whether or not a genome shall be a candidate for downloaded if it isn't marked in the database as either a reference genome or a representative genome. This is helpful if you don't want to allow "partial genomes" etc.

skip_bacteria

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.

release

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.

gunzip

a logical, indicating whether or not files should be unzipped.

path

a character string specifying the location (a folder) in which the corresponding CDS file shall be stored. Default is path = file.path("_ncbi_downloads","CDS").

mute_citation

logical, default FALSE, indicating whether citation message should be muted.

Value

File path to downloaded genome.

Details

Fetching of assembly / sequence data is done by fetching an overview file from metadata of given database:
For NCBI (refseq/genbank):
Internally this function loads the the overview.txt file from NCBI:

refseq: ftp.ncbi.nlm.nih.gov/genomes/refseq/

genbank: ftp.ncbi.nlm.nih.gov/genomes/genbank/

It will then create a directory relative to file type wanted, if you get fasta genomes it will be _ncbi_downloads/genomes' etc. 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.

For ensembl it fetches overview per type from the rest API:

ensembl: https://rest.ensembl.org

See also

Other getBio: getBio(), getCollection(), getGFF(), getGenome(), getProteome(), getRNA()

Other cds: getCDSSet(), read_cds()

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# download the genome of Arabidopsis thaliana from refseq
# and store the corresponding genome CDS file in '_ncbi_downloads/CDS'
file_path <- getCDS( db       = "refseq",
             organism = "Arabidopsis thaliana",
             path     = file.path("_ncbi_downloads","CDS"))

Ath_CDS <- read_cds(file_path, format = "fasta")

} # }