Skip to contents

Genome Annotation Retrieval (GFF3)

Source: R/getGFF.R
getGFF.Rd

Main retrieval function for GFF files of an organism of interest. By specifying the scientific name of an organism of interest the corresponding gff file storing the annotation for the organism of interest can be downloaded and stored locally. GFF files can be retrieved from several databases.

Usage

getGFF(
  db = "refseq",
  organism,
  reference = FALSE,
  release = NULL,
  gunzip = FALSE,
  remove_annotation_outliers = FALSE,
  path = file.path("_ncbi_downloads", "annotation")
)

Arguments

db

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

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

organism

a character string specifying the scientific name of the organism of interest, e.g. organism = "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.

remove_annotation_outliers

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.

path

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

Value

File path to downloaded annotation file.

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 '_ncbi_downloads/annotation' to store the genome of interest as fasta file for future processing. In case the corresponding fasta file already exists within the '_ncbi_downloads/annotation' folder and is accessible within the workspace, no download process will be performed.

See also

getProteome, getCDS, getGenome, getRNA, getRepeatMasker, getAssemblyStats, meta.retrieval

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# download the annotation of Arabidopsis thaliana from refseq
# and store the corresponding genome file in '_ncbi_downloads/annotation'
getGFF( db       = "refseq", 
               organism = "Arabidopsis thaliana", 
               path = file.path("_ncbi_downloads","annotation"))


# download the genome of Arabidopsis thaliana from genbank
# and store the corresponding genome file in '_ncbi_downloads/annotation'
getGFF( db       = "genbank", 
               organism = "Arabidopsis thaliana", 
               path = file.path("_ncbi_downloads","annotation"))

}