Get the Latest Gencode Release Dynamically

This function retrieves the latest available release of the Gencode database for a given species (human or mouse) by querying the relevant FTP directory. It automates the process of identifying the latest release of annotations for human or mouse.

Usage

get_latest_release(species, verbose = TRUE)

Arguments

species

A character string indicating the species. Supported values are:

• "human"

• "mouse"

verbose

Logical. If TRUE (default), the function prints the latest release.

Value

A character string representing the latest release version for the specified species (e.g., "release_42" for human or "release_36" for mouse).

Details

The function accesses the GENCODE FTP directory and parses the available folders to determine the latest release. It is particularly useful for bioinformatics workflows that require up-to-date annotation files without manual checks.

Examples

# Retrieve the latest release version for human
human_release <- get_latest_release(species = "human", verbose = FALSE)
cat("Latest human GENCODE release: release_47")
#> Latest human GENCODE release: release_47

# Get the latest release for mouse
mouse_release <- get_latest_release("mouse", verbose = TRUE)
#> Error in function (type, msg, asError = TRUE) {    if (!is.character(type)) {        i = match(type, CURLcodeValues)        typeName = if (is.na(i))             character()        else names(CURLcodeValues)[i]    }    typeName = gsub("^CURLE_", "", typeName)    fun = (if (asError)         stop    else warning)    fun(structure(list(message = msg, call = sys.call()), class = c(typeName,         "GenericCurlError", "error", "condition")))}(7L, "Failed to connect to ftp.ebi.ac.uk port 443 after 375 ms: Couldn't connect to server",     TRUE): Failed to connect to ftp.ebi.ac.uk port 443 after 375 ms: Couldn't connect to server