tests/testthat/test_a_utils.R

In ngstk: Next-Generation Sequencing (NGS) Data Analysis Toolkit

test_that("set_tools", {
  config.file <- system.file("extdata", "demo/tools_config.json", package = "ngstk")
  config.list <- list(gatk = "/path/gatk")
  config.vec <- c("/path/samtools")
  names(config.vec) <- "samtools"
  tools <- set_tools(config.file, config.list, config.vec, eval.params = list(config = "tools"))
  expect_that(is.list(tools), equals(TRUE))
  expect_that(length(tools), equals(3))
  expect_that(names(tools)[1], equals("gmap"))
})

test_that("set_colors", {
  red_blue <- set_colors("red_blue")
  expect_that(length(red_blue) > 0, equals(TRUE))
  default <- set_colors("default")
  expect_that(length(default) > 0, equals(TRUE))
  colors <- set_colors(show_all_themes = TRUE)
  expect_that(is.list(colors), equals(TRUE))
})

test_that("batch_file", {
  dat <- data.frame(a = 1:100, b = 1:100)
  filename <- tempfile()
  write.table(dat, filename, sep = "\t", row.names = F, quote = F)
  handler_fun <- function(x, i = 1, ...) {
    return(x[i])
  }
  x <- batch_file(filename = filename, batch_lines = 10, handler = handler_fun)
  expect_that(x[[1]], equals("a\tb"))
  x <- batch_file(filename = filename, batch_lines = 10, handler = handler_fun, 
    extra_fread_params = list(sep = "\t", header = FALSE, return_1L = FALSE))
  x <- rbindlist(x)
  expect_that(nrow(x), equals(10))
})