SRA Run Metadata Utilities — sra_runinfo • RWisecondorX

These helpers standardize how RWisecondorX stages SRA run metadata for conformance fixtures. They use the NCBI SRA backend runinfo endpoint and default to writing project metadata into inst/extdata/ in the source tree.

Usage

sra_runinfo_url(accession, mode = c("acc", "term"))

download_sra_runinfo(
  accession,
  dest = file.path("inst", "extdata", paste0(accession, "_runinfo.csv")),
  overwrite = FALSE,
  quiet = TRUE,
  mode = c("acc", "term"),
  downloader = utils::download.file
)

read_sra_runinfo(
  accession,
  path = system.file("extdata", paste0(accession, "_runinfo.csv"), package =
    "RWisecondorX")
)

Arguments

accession: A study or project accession such as PRJNA400134.
mode: Retrieval mode. "acc" queries the backend with acc=<accession>; "term" queries with term=<accession>.
dest: Output CSV path. Defaults to inst/extdata/<accession>_runinfo.csv in the current source checkout.
overwrite: Logical; overwrite an existing file.
quiet: Logical; passed through to the downloader.
downloader: Function used to retrieve the URL. Defaults to utils::download.file(). This is injectable so tests can avoid network calls.
path: Path to the run metadata CSV. Defaults to the bundled file under inst/extdata/<accession>_runinfo.csv.

Value

sra_runinfo_url() returns a length-1 character URL. download_sra_runinfo() returns the output path, invisibly. read_sra_runinfo() returns a data.frame.

Details

The SRA Run Selector and backend runinfo endpoints can expose slightly different columns. For reproducible package fixtures, RWisecondorX standardizes on the backend runinfo CSV output.

Examples

sra_runinfo_url("PRJNA400134")
#> [1] "https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/runinfo?acc=PRJNA400134"

if (FALSE) { # \dontrun{
download_sra_runinfo("PRJNA400134")
metadata <- read_sra_runinfo("PRJNA400134")
} # }