How to ungz various .gz files kept in different folders?

Question

I have various .gz files kept in different folders. A sample of the order of files is mentioned below. I want to ungz them and want them to be in the same folder as before (e.g. .gz files of Folder 1a should be remain in Folder 1a upon ungz-ing) and delete the .gz files later.

Folder1
 Folder 1a > many .gz files
 Folder 2a > many .gz files
 Folder 3a > many .gz files
 .
 .
 .

I know how to unzip .zip files but that does not seem to work for .gz files. I want to do it in R, can anyone please help. I am working in Windows.

Answer 1

First write a function to decompress a single file. The gzfile() function can be used to open a connection that decompresses a gzip file.

decompress <- function(file, dest = sub("\\.gz$", "", file)) {
  # Set up source and destination connections
  src <- gzfile(file, "rb")
  on.exit(close(src), add = TRUE)
  dst <- file(dest, "wb")
  on.exit(close(dst), add = TRUE)
  
  # Copy decompressed contents from source to destination
  BATCH_SIZE <- 10 * 1024^2
  repeat {
    bytes <- readBin(src, raw(), BATCH_SIZE)
    if (length(bytes) != 0) {
      writeBin(bytes, dst)
    } else {
      break
    }
  }
  
  invisible(dest)
}

Then, apply it to the files you want to decompress:

files <- list.files(pattern = "*.gz", full.names = TRUE, recursive = TRUE)
for (file in files) {
  decompress(file)
}

Answer 2

If you are in Linux, you can use find command in the top folder to find all the .gz files, and them redirect all the results to gzip command (with -d option indicating that you want to decompress) as follows:

find . -name "*.gz" -exec gzip -d {} \;

In Windows try:

gzip -r -d Folder1

To do it in R, use system function to execute one of the two above commands.