tests/testthat/test-parse-to-file.R

In UW-GAC/wgsaparsr: A R package for Parsing Annotation File for Database Import

context("test_parse-to-file - unit tests")

test_that("parse_to_file() selects SNV fields", {
  source_tmp <- tempfile()
  snv_tmp <- tempfile()
  on.exit(unlink(snv_tmp))
  on.exit(unlink(source_tmp))

  source_content <-
    c("chr\tpos\tref\talt\tHeader 1\tHeader 2\tHeader 3",
      "1\t123\tA\tG\tfoo\tbar\tbat")

  readr::write_lines(source_content, source_tmp)

  source_file <- source_tmp

  config <-
    tibble::tibble(
      field = c("Header 1", "Header 3"),
      SNV = c(TRUE, TRUE),
      indel = c(FALSE, FALSE),
      dbnsfp = c(FALSE, FALSE),
      pivotGroup = c(NA, NA),
      pivotChar = c(NA, NA),
      parseGroup = c(NA, NA),
      transformation = c(NA, NA),
      toRemove = c(NA, NA)
    )
  destination <- snv_tmp

  parse_to_file(source_file = source_file,
                 config = config,
                 destination = snv_tmp,
                 dbnsfp_destination = NA,
                 chunk_size = 10000,
                 header_file = NA,
                 verbose = FALSE)

  written <- readr::read_lines(snv_tmp, progress = FALSE)
  expect_equal(written, c("Header 1\tHeader 3", "foo\tbat"))
})