Download ENCODE files

Download files from an ENCODE file table, selected-file object, file search, or file accession. Planned sizes are checked before transfer, existing files are not overwritten by default, files are written through a unique temporary .part path, and size/MD5 checks are used when ENCODE provides the metadata.

Usage

encode_download(
  x,
  file_accession = NULL,
  file_format = NULL,
  output_type = NULL,
  assembly = NULL,
  status = "released",
  limit = NULL,
  directory = NULL,
  max_file_size = "250MB",
  max_total_size = "500MB",
  allow_unknown_size = FALSE,
  overwrite = FALSE,
  dry_run = FALSE,
  prefer_cloud = FALSE,
  verify = c("md5", "size"),
  quiet = FALSE
)

Arguments

x

ENCFF accession(s), file metadata table, file search result, selected-file object, or ENCSR experiment accession(s). ENCSR input is first passed to encode_list_files().

file_accession

Optional ENCODE file accession(s), such as "ENCFF260OJQ", to download from x. Use this when you want specific files rather than the first limit rows.

file_format

Optional file-format filter used when x is an ENCSR experiment accession.

output_type

Optional output-type filter used when x is an ENCSR experiment accession.

assembly

Optional genome-assembly filter used when x is an ENCSR experiment accession.

status

Optional file-status filter used when x is an ENCSR experiment accession.

limit

Optional number of files to use from the top of x.

directory

Destination directory. If NULL, a package cache directory from tools::R_user_dir("encodeUtils", "cache") is used. Supply an explicit project directory for reusable data.

max_file_size

Maximum ENCODE-reported size accepted per file during planning, as bytes or a string like "500MB". The observed size is checked after transfer when size verification is enabled.

max_total_size

Maximum total ENCODE-reported size accepted during planning, as bytes or a string.

allow_unknown_size

Whether to allow real downloads for files whose ENCODE metadata do not include file_size. Dry-runs are always allowed and report the unknown-size count.

overwrite

Whether existing destination files may be replaced.

dry_run

If TRUE, return the planned download table without downloading.

prefer_cloud

Whether to prefer ENCODE cloud URLs when available.

verify

Verification checks to perform. Supported values are "md5" and "size". Use NULL to record downloads without size or MD5 verification.

quiet

If FALSE, print concise progress messages.

Value

An encode_download_result data frame. Dry runs return planned rows with destination local_path, known-size totals, unknown-size counts, and download_status = "planned". Transfers return one row per file with download_status, downloaded_at, downloaded_size, the expected md5sum, observed_md5, verification flags, and failure_reason. Printing the result shows the transfer status and local destination; use encode_results() for the complete table.

Examples

plan <- encode_download(
    "ENCFF859GWB",
    directory = tempdir(),
    dry_run = TRUE,
    quiet = TRUE
)

encode_results(plan)
#> ENCODE download
#> - files: 1
#> - experiments: 1
#> - known total size: 59.54 KB
#> Download records:
#>         file format                   output file_size download
#>  ENCFF859GWB    tsv microRNA quantifications  59.54 KB  planned
#>                             path
#>  /tmp/Rtmpi8WRPd/ENCFF859GWB.tsv