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Generic Bio data set extractor

Source: R/getBioSet.R
getBioSet.Rd

Usually you want to use one of the specific set extractors

Usage

getBioSet(
  db = "refseq",
  organisms,
  set_type,
  reference = FALSE,
  release = NULL,
  gunzip = TRUE,
  update = FALSE,
  skip_bacteria = TRUE,
  path = paste0("set_", toupper(set_type)),
  remove_annotation_outliers = FALSE,
  assembly_type = "toplevel",
  format = "gff3",
  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:

set_type

the biological sequence type that shall be retrieved. Available options are

  • set_type = "genome"

  • set_type = "proteome"

  • set_type = "cds"

  • set_type = "gff"

  • set_type = "rna"

  • set_type = "assembly_stats"

  • set_type = "repeat_masker"

  • set_type = "collection" (all the others)

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

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.

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 Only set to TRUE, if you believe you cache is outdated (Species only exist in newest release etc)

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.

path

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

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.

assembly_type

character, default c("primary_assembly", "toplevel"). Used for ensembl only, specifies the genome assembly type. Searches for both primary and toplevel, and if both are found, uses the first by order (so primary is prioritized by default). The Primary assembly should usually be used if it exists. The "primary assembly" contains all the top-level sequence regions, excluding alternative haplotypes and patches. If the primary assembly file is not present for a species (only defined for standard model organisms), that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: ensembl tutorial

format

"gff3", alternative "gtf" for ensembl.

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

getBio

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

Author

Hajk-Georg Drost

Examples

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