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Download GFF3 File from the GENCODE Database

Source: R/files.R
get_gff3.Rd

Downloads a GFF3 file for a specified species, release version, and annotation type from the GENCODE database. The file is saved to a user-specified directory or the current working directory by default.

Usage

get_gff3(species, release_version, annotation_type, dest_folder)

Arguments

species

A character string indicating the species. Supported values are:

  • "human"

  • "mouse"

release_version

A character string specifying the release version. Options include:

  • "latest_release": Fetches the latest release for the species.

  • "release_X": Specific release version for human (e.g., "release_42").

  • "release_MX": Specific release version for mouse (e.g., "release_M36").

annotation_type

A character string specifying the annotation type. Supported values include:

  • "annotation.gff3.gz"

  • "basic.annotation.gff3.gz"

  • "chr_patch_hapl_scaff.annotation.gff3.gz"

  • "chr_patch_hapl_scaff.basic.annotation.gff3.gz"

  • "long_noncoding_RNAs.gff3.gz"

  • "primary_assembly.annotation.gff3.gz"

  • "primary_assembly.basic.annotation.gff3.gz"

  • "tRNAs.gff3.gz"

  • "polyAs.gff3.gz"

dest_folder

A character string specifying the destination folder. Defaults to the current working directory.

Value

A character string specifying the full path of the downloaded GFF3 file.

Details

The function dynamically determines the correct file URL based on the provided parameters and downloads the GFF3 file to the desired location. If "latest_release" is specified for release_version, the function will first determine the latest available release using get_latest_release().

Examples

# \donttest{
# Download the latest human GTF file with primary assembly annotations into a temp directory
temp_dir <- tempdir()
gff3_file <- get_gff3(
  species = "human",
  release_version = "latest_release",
  annotation_type = "primary_assembly.basic.annotation.gff3.gz",
  dest_folder = temp_dir
)
#> Latest human GENCODE release: release_48
#> Downloading GFF3 file from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.primary_assembly.basic.annotation.gff3.gz
#> Warning: URL 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.primary_assembly.basic.annotation.gff3.gz': status was 'Couldn't connect to server'
#> Error downloading file: cannot open URL 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.primary_assembly.basic.annotation.gff3.gz'
#> Error in get_gff3(species = "human", release_version = "latest_release",     annotation_type = "primary_assembly.basic.annotation.gff3.gz",     dest_folder = temp_dir): Failed to download the GFF3 file. Please check the URL or your internet connection.
print(gff3_file)
#> Error: object 'gff3_file' not found

# Download a specific mouse release with long noncoding RNA annotations into a temp directory
temp_dir <- tempdir()
gff3_file <- get_gff3(
  species = "mouse",
  release_version = "release_M36",
  annotation_type = "long_noncoding_RNAs.gff3.gz",
  dest_folder = temp_dir
)
#> Downloading GFF3 file from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M36/gencode.vM36.long_noncoding_RNAs.gff3.gz
#> Warning: URL 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M36/gencode.vM36.long_noncoding_RNAs.gff3.gz': status was 'Couldn't connect to server'
#> Error downloading file: cannot open URL 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M36/gencode.vM36.long_noncoding_RNAs.gff3.gz'
#> Error in get_gff3(species = "mouse", release_version = "release_M36",     annotation_type = "long_noncoding_RNAs.gff3.gz", dest_folder = temp_dir): Failed to download the GFF3 file. Please check the URL or your internet connection.
print(gff3_file)
#> Error: object 'gff3_file' not found
# }