tests/testthat/test-uscs.R

In sdangelis/sdamisc: A convenience package bringing together commonly used R functions

test_that("We can query UCSC", {
  expect_equal(
    sdamisc::queryUcsc(
      "SELECT chrom,chromStart,chromEnd FROM centromeres LIMIT 1"
    ),
    data.frame("chrom" = "chr1", "chromStart" = 122026459, "chromEnd" = 122224535)
  )
  expect_equal(
    sdamisc::queryUcsc(
      "SELECT chrom,chromStart,chromEnd FROM centromeres WHERE chrom in (?) LIMIT 2",
      list("chr1")
    ), data.frame(
      "chrom" = "chr1", "chromStart" = c(122503247, 122026459),
      "chromEnd" = c(124785432, 122224535)
    )
  )
  expect_equal(
    sdamisc::queryUcsc(
      "SELECT DISTINCT chrom FROM centromeres WHERE chrom in (?)",
      list(c("chr1", "chr2"))
    ),
    data.frame("chrom" = c("chr1", "chr2"))
  )
  # bad query
  expect_error(sdamisc::queryUcsc("SELECT chrom centromeres LIMIT 1"))
})