biomartr (version 0.9.0)

getCDSSet: CDS retrieval of multiple species

Description

Main CDS retrieval function for a set of organism of interest. By specifying the scientific names of the organisms of interest the corresponding fasta-files storing the CDS of the organisms of interest will be downloaded and stored locally. CDS files can be retrieved from several databases.

Usage

getCDSSet(db = "refseq", organisms, reference = FALSE,
  release = NULL, clean_retrieval = TRUE, gunzip = TRUE,
  update = FALSE, path = "set_CDS")

Arguments

db

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

• db = "refseq"

• db = "genbank"

• db = "ensembl"

organisms

a character vector storing the names of the organisms than shall be retrieved. There are three available 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 CDS shall be downloaded if it isn't marked in the database as either a reference CDS or a representative CDS.

release

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

clean_retrieval

logical value indicating whether or not downloaded files shall be renamed for more convenient downstream data analysis.

gunzip

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

update

a logical value indicating whether or not files that were already downloaded and are still present in the output folder shall be updated and re-loaded (update = TRUE or whether the existing file shall be retained update = FALSE (Default)).

path

a character string specifying the location (a folder) in which the corresponding CDSs shall be stored. Default is path = "set_CDS".

Value

File path to downloaded CDSs.

Details

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.

See Also

getGenomeSet, getProteomeSet, getRNASet, getGFFSet, getCDS, getGFF, getRNA, meta.retrieval, read_cds

Examples

# NOT RUN {
getCDSSet("refseq", organisms = c("Arabidopsis thaliana", 
                                  "Arabidopsis lyrata", 
                                  "Capsella rubella"))
# }
# NOT RUN {
# }