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

Source: R/getCollectionSet.R
getCollectionSet.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.

Usage

getCollectionSet(
  db = "refseq",
  organisms,
  reference = FALSE,
  release = NULL,
  clean_retrieval = FALSE,
  gunzip = TRUE,
  update = FALSE,
  remove_annotation_outliers = TRUE,
  path = "set_collections"
)

Arguments

db

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

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

organisms

a character vector storing the scientific names of the organisms for which collections shall be retrieved. 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 collection 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.

clean_retrieval,

a logical, default FALSE. Cleaning file names for more convenient downstream processing.

gunzip

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

update

a logical, default FALSE. The existing file will be retained if existing. If TRUE, will download and overwrite the file.

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 collection shall be stored. Default is path = file.path("_db_downloads","collections").

Value

File path to downloaded genome.

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

See also

getCollection, getGenomeSet, getProteomeSet, getCDSSet, getGenome, getProteome, getCDS, getGFF, getRNA, meta.retrieval, read_genome

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# define scientific names of species for which
# collections shall be retrieved
organism_list <- c("Arabidopsis thaliana",
                   "Arabidopsis lyrata",
                   "Capsella rubella")
# download the collection of Arabidopsis thaliana from refseq
# and store the corresponding genome file in '_ncbi_downloads/collection'
 getCollectionSet( db       = "refseq",
             organism = organism_list,
             path = "set_collections")
}