Nothing
#' Sort methylation file
#' @keywords internal
#'
#' @param x the path to the methylation file to sort
#'
#' @return invisibly returns path of sorted file
sort_methy_file <- function(x) {
assert_that(is.readable(x))
if (.Platform$OS.type == "windows") {
methy_df <- readr::read_tsv(
x,
col_names = methy_col_names(),
col_types = methy_col_types())
methy_df <- dplyr::arrange(methy_df, .data$chr, .data$pos)
readr::write_tsv(methy_df, x, col_names = FALSE)
} else {
cmd <- glue::glue("sort -k2,3V {x} -o {x}")
system(cmd)
}
invisible(x)
}
tabix_compress <- function(x, index = TRUE) {
assert_that(is.readable(x))
f <- Rsamtools::bgzip(x, overwrite = TRUE)
if (index) {
tabix_index(f)
}
f
}
tabix_index <- function(x) {
assert_that(is.readable(x))
Rsamtools::indexTabix(x, seq = 2, start = 3, end = 3)
}
#' Convert methylation file to tabix format
#' @keywords internal
#'
#' @param x the path to the sorted methylation file
#'
#' @return invisibly returns the path to the tabix file
raw_methy_to_tabix <- function(x) {
assert_that(is.readable(x))
bgz_name <- tabix_compress(x)
tabix_index(bgz_name)
invisible(bgz_name)
}
#' Create a tabix file using methylation calls
#'
#' @param input_files the files to convert
#' @param output_file the output file to write results to (must end in .bgz)
#' @param samples the names of samples corresponding to each file
#' @param verbose TRUE if progress messages are to be printed
#'
#' @return invisibly returns the output file path, creates a tabix file (.bgz)
#' and its index (.bgz.tbi)
#' @export
#'
#' @examples
#' methy_calls <- system.file(package = "NanoMethViz",
#' c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"))
#' temp_file <- paste0(tempfile(), ".tsv.bgz")
#'
#' create_tabix_file(methy_calls, temp_file)
create_tabix_file <- function(
input_files,
output_file,
samples = extract_file_names(input_files),
verbose = TRUE
) {
assert_that(
is.character(input_files),
is.string(output_file),
tools::file_ext(output_file) == "bgz",
is.character(samples),
length(input_files) == length(samples)
)
if (.Platform$OS.type == "windows") {
timed_log("WARNING: creating tabix file on windows requires at least twice as much memory as total size of methylation data")
}
temp_file <- tempfile()
if (verbose) {
timed_log("creating methylation table")
}
convert_methy_format(input_files, temp_file, samples, verbose = verbose)
if (verbose) {
timed_log("sorting methylation table")
}
sort_methy_file(temp_file)
if (verbose) {
timed_log("compressing methylation table to tabix with index")
}
raw_methy_to_tabix(temp_file)
fs::file_move(paste0(temp_file, ".bgz"), output_file)
fs::file_move(paste0(temp_file, ".bgz.tbi"), paste0(output_file, ".tbi"))
fs::file_delete(temp_file)
invisible(output_file)
}
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