R/bsubset.R

In MagicHead99/bread: Analyze Big Files Without Loading Them in Memory

#' Pre-subsets rows of a data file by index number before loading it in memory
#'
#' Simple wrapper for data.table::fread() allowing to subset rows of data from a file
#' with the Unix 'sed' or 'awk' commands. This method is useful if you want to load a file
#' too large for your available memory (and encounter the 'cannot allocate vector of size' error).
#' You need to input the index number of the first and last rows you want to load in memory with fread(),
#' or alternatively use either the head or tail arguments to subset the first or last rows of the file.
#'
#' @param file String. Full path to a file
#' @param first_row Numeric. First row of the portion of the file to subset.
#' @param last_row Numeric. Last row of the portion of the file to subset.
#' @param head Numeric. How many rows starting from the first in the file.
#' @param tail Numeric. How many rows starting from the last in the file.
#' @param ... Arguments that must be passed to data.table::fread() like 'sep'.
#' @keywords big file subset sed awk allocate vector size
#' @return A dataframe containing the subsetted rows
#' @examples
#' file <- system.file('extdata', 'test.csv', package = 'bread')
#' ## Head or Tail... for the first n or last n rows
#' bsubset(file = file, head = 5)
#' ## Subset from the middle of a file
#' bsubset(file = file, first_row = 5, last_row = 10)
#' ## first_row defaults as 1 and last_row as the last row of the file
#' bsubset(file = file, first_row = 5)
#' bsubset(file = file, last_row = 10)
#' @export

bsubset <- function(file = NULL,
                    head = NULL, tail = NULL,
                    first_row = NULL, last_row = NULL,
                    ...){

  args = list(...)

  ## Getting full path, in case the file is in the wd
  file <- normalizePath(path = file)
  if(startsWith(file, "\\")){
    file <- gsub(pattern = "\\\\", replacement = "/", x = file)
  }
  ## Quoting the file to prevent errors due to special characters like ')'
  ## according to environment
  if(.Platform$OS.type == 'windows'){
    qfile <- shQuote(file, type = 'cmd2')
    ## More quoting to manage filepaths with spaces
    qfile <- paste0('\'', qfile, '\'')
  } else if(.Platform$OS.type == 'unix'){
    qfile <- shQuote(file)
  }

  meta_output <- list()
  meta_output$colnames <- bcolnames(file, ...)


  unixCmdStr <- bsubsetStr(file = file, head = head, tail = tail,
                           first_row = first_row, last_row = last_row,
                           ...)
  unixCmdStr <- paste(unixCmdStr, qfile)

  args <- c(cmd = unixCmdStr, args)
  df <- do.call(data.table::fread, args)
  ## sed / awk loses the colnames, we put them back on
  colnames(df) <- meta_output$colnames

  return(df)
}