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GFF retrieval of multiple species

Source: R/getSet.R
getGFFSet.Rd

Main GFF 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 GFF of the organisms of interest will be downloaded and stored locally. GFF files can be retrieved from several databases.

Usage

getGFFSet(
  db = "refseq",
  organisms,
  reference = FALSE,
  release = NULL,
  skip_bacteria = TRUE,
  gunzip = TRUE,
  remove_annotation_outliers = FALSE,
  update = FALSE,
  format = "gff3",
  path = "set_GFF",
  mute_citation = FALSE
)

Arguments

db

a character string specifying the database from which the genome 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:

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.

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.

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.

gunzip

a logical, 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.

update

logical, default FALSE. Updated backend cached files needed. Usually keep this false, to make ut run much faster. Only set to TRUE, if you believe you cache is outdated (Species only exist in newest release etc)

format

"gff3", alternative "gtf" for ensembl.

path

character, default location is paste0("set_", toupper(set_type))

mute_citation

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

Value

character vector, the file path to the downloaded genomes,
The returned character vector has names as either:
- 'new' (file was downloaded now)
- 'old' files did already exist)

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 getBioSet: getBioSet(), getCDSSet(), getCollectionSet(), getGenomeSet(), getProteomeSet(), getRNASet()

Other gff: getGFF(), read_gff()

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
getBioSet("refseq", organisms = c("Arabidopsis thaliana",
                                  "Arabidopsis lyrata",
                                  "Capsella rubella"),
                                  set_type = "cds")
} # }