biomartr (version 0.9.0)

getCDS: Coding Sequence Retrieval

Description

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, release = NULL,
  gunzip = FALSE, path = file.path("_ncbi_downloads", "CDS"))

Arguments

db

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

• db = "refseq"

• db = "genbank"

• db = "ensembl"

organism

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 downloaded if it isn't marked in the database as either a reference genome or a representative genome.

release

the database release version of ENSEMBL (db = "ensembl"). Default is release = NULL meaning that the most recent database version is used.

gunzip

a logical value 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").

Value

File path to downloaded CDS file.

See Also

getGenome, getProteome, getGFF, getRNA, getRepeatMasker, getAssemblyStats, meta.retrieval, read_cds

Examples

# NOT RUN {
# 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")

# }