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Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats

Source: R/getCollection.R
getCollection.Rd

Main collection retrieval function for an organism of interest. By specifying the scientific name of an organism of interest a collection consisting of the genome file, proteome file, CDS file, RNA file, GFF file, Repeat Masker file, AssemblyStats file of the organism of interest can be downloaded and stored locally. Collections can be retrieved from several databases. For full set of collection elements, see: biomartr:::supported_biotypes(db)

Usage

getCollection(
  db = "refseq",
  organism,
  reference = TRUE,
  skip_bacteria = TRUE,
  release = NULL,
  assembly_type = "toplevel",
  analyse_genome = FALSE,
  remove_annotation_outliers = FALSE,
  gunzip = FALSE,
  path = file.path("_db_downloads", "collections"),
  mute_citation = FALSE
)

Arguments

db

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

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

organism

Organism selector id, 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 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.

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.

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.

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

analyse_genome

logical, default FALSE. If TRUE, get general genome statistics like gc content etc. For more details, see ?summary_genome

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.

gunzip

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

path

a character string specifying the location (a folder) in which the corresponding collection shall be stored. Default is path = file.path("_db_downloads","collections").

mute_citation

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

Value

File path to downloaded genome.

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 getBio: getBio(), getCDS(), getGFF(), getGenome(), getProteome(), getRNA()

Other collection: getCollectionSet()

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# download the collection of Homo sapiens from refseq
# and store the corresponding genome file in '_ncbi_downloads/collection'
 Hsap_collection <- getCollection( db       = "refseq",
             organism = "Homo sapiens",
             path = file.path("_db_downloads","collections"))
# download the collection of Homo sapiens from genbank
# and store the corresponding genome file in '_ncbi_downloads/collection'
 Hsap_collection <- getCollection( db       = "genbank",
             organism = "Homo sapiens",
             path = file.path("_db_downloads","collections"))
# download the collection of Homo sapiens from ensembl
# and store the corresponding genome file in '_ncbi_downloads/collection'
 Hsap_collection <- getCollection( db       = "ensembl",
             organism = "Homo sapiens",
             path = file.path("_db_downloads","collections"))
} # }