Download sequence or annotation from ENSEMBL — getENSEMBL • biomartr
Description: Backend function for retrieving files sequence and annotation files from the ENSEMBL ftp server

# Download sequence or annotation from ENSEMBL

Source: `R/ensembl_ftp_generics.R`
`getENSEMBL.Rd`

Backend function for retrieving files sequence and annotation files from the ENSEMBL ftp server

    getENSEMBL(
      organism,
      type = "dna",
      id.type = "toplevel",
      release = NULL,
      path,
      format
    )

## Arguments

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`)

type

  character, biological sequence type (e.g. "dna", "cds")

id.type

  a character, default "toplevel". id type of assembly, either "toplevel" or "primary_assembly" usually.

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.

path

  location where file shall be stored.

format

  "gff3", alternative "gtf" for ensembl.

## Value

either a character path to downloaded file, or a logical FALSE, specifying failure.

## Author

Hajk-Georg Drost