R/system.R

In liutiming/dfGenomicRanges:

#' write a table contains a chromosome column (assume unique) and use the chr as a part of file name
#' @export
write_chr_tbl <- function(chr_tbl, prefix, suffix, delim, col_names) {
  chr <- dplyr::distinct(chr_tbl, chr) %>% dplyr::pull() %>% as.character()
  if (length(chr) > 1) {
    stop("more than one chromosome in the column `chr`")
  }
  file_name <- glue::glue("{prefix}{chr}{suffix}")
  vroom::vroom_write(chr_tbl, path = file_name, delim = delim, col_names = col_names)
  return(file_name)
}

#' plink 2 general command
#' @export

plink2_bfile_general <- function(input, chr, prefix, argument) {
  bfile  <- stringr::str_replace(input, ".bed", "") %>%
    stringr::str_replace(".bim", "")
  command <- glue::glue("plink2 --threads 16 --bfile {bfile} {argument} --make-bed --out {prefix}{chr}")
  system(command)
  output <- glue::glue("{prefix}{chr}.bim")
  return(output)
}