tests/testthat/test_trimming.R

In mammerlin/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

context("trim.mott function")
data(drosophila)


test_that("input variables", {
  expect_error(trim.mott("this is not abif"), "abif.seq must be an")
  expect_error(trim.mott("", "egg"), "cutoff must be a")
  expect_error(trim.mott("", "-1"), "cutoff must be a")
})

test_that("trimming works", {
    r1 = trim.mott(drosophila[[1]], 1000) # shouldn't trim anything
    expect_equal(r1$start, 1)
    expect_equal(r1$finish, length(drosophila[[1]]@data$PCON.2))

    r2 = trim.mott(drosophila[[1]]) # default trims a bit
    expect_equal(r2$start, 27)
    expect_equal(r2$finish, 477)
})

test_that("extreme examples", {
    # a bug I found with the following quality scores
    # this used to give start = 560, finish = 1
    # it SHOULD give start = 0, finish = 0
    q = c(8, 3, 4, 4, 4, 4, 7, 6, 7, 7, 7, 5, 7, 5, 5, 10, 5, 4, 4, 5, 6, 8, 8, 7, 10, 7, 15, 8, 10, 9, 16, 10, 6, 8, 7, 8, 20, 12, 6, 8, 14, 29, 27, 34, 34, 26, 15, 28, 15, 15, 32, 32, 13, 10, 12, 12, 18, 4, 12, 22, 28, 16, 12, 22, 15, 35, 25, 32, 13, 11, 13, 10, 13, 25, 13, 23, 23, 11, 29, 19, 24, 24, 18, 30, 11, 23, 27, 13, 22, 15, 7, 13, 22, 13, 12, 18, 10, 12, 7, 13, 8, 18, 22, 18, 13, 12, 30, 12, 11, 10, 4, 4, 6, 10, 11, 11, 8, 13, 10, 12, 11, 9, 7, 8, 12, 13, 10, 24, 10, 10, 8, 9, 8, 7, 12, 13, 25, 25, 12, 20, 13, 24, 20, 8, 13, 13, 11, 13, 8, 20, 12, 12, 13, 11, 13, 10, 11, 12, 11, 8, 12, 5, 23, 13, 25, 10, 16, 15, 21, 17, 11, 10, 10, 10, 10, 12, 12, 12, 22, 18, 12, 13, 10, 13, 10, 24, 21, 14, 14, 18, 22, 24, 12, 12, 24, 18, 12, 23, 8, 8, 27, 18, 13, 22, 13, 13, 12, 17, 9, 21, 13, 13, 12, 20, 8, 11, 12, 13, 16, 18, 17, 12, 23, 12, 12, 11, 5, 10, 12, 11, 24, 8, 22, 8, 10, 13, 16, 10, 12, 12, 11, 12, 12, 18, 12, 23, 18, 8, 13, 13, 18, 9, 12, 13, 20, 22, 10, 8, 8, 12, 12, 12, 9, 18, 22, 13, 21, 11, 15, 13, 12, 18, 15, 17, 15, 12, 12, 12, 12, 6, 6, 16, 8, 18, 14, 13, 12, 14, 19, 12, 13, 12, 9, 12, 6, 11, 9, 11, 13, 13, 32, 32, 27, 27, 12, 7, 8, 6, 16, 11, 13, 10, 8, 17, 18, 18, 23, 7, 13, 8, 24, 10, 15, 10, 12, 13, 8, 6, 10, 12, 15, 9, 13, 12, 13, 13, 11, 8, 9, 11, 12, 12, 9, 13, 6, 12, 12, 8, 11, 10, 11, 12, 22, 11, 23, 16, 23, 9, 8, 10, 20, 9, 15, 10, 10, 12, 6, 11, 10, 13, 26, 11, 12, 27, 18, 20, 13, 27, 11, 13, 27, 6, 26, 6, 13, 11, 23, 12, 24, 12, 9, 18, 18, 14, 30, 17, 21, 27, 27, 18, 23, 27, 21, 18, 13, 12, 18, 12, 25, 22, 8, 8, 13, 23, 12, 11, 17, 26, 20, 12, 30, 15, 30, 19, 19, 18, 34, 15, 20, 36, 29, 24, 27, 18, 13, 24, 18, 12, 8, 6, 18, 12, 8, 32, 5, 17, 8, 10, 18, 27, 27, 30, 39, 36, 37, 26, 26, 18, 24, 26, 24, 35, 31, 28, 15, 13, 13, 24, 19, 12, 27, 8, 8, 6, 10, 18, 5, 27, 10, 37, 21, 13, 18, 12, 19, 13, 10, 12, 19, 13, 10, 18, 22, 21, 18, 18, 22, 26, 30, 34, 14, 11, 5, 5, 4, 9, 11, 9, 11, 13, 24, 13, 11, 9, 10, 15, 11, 23, 18, 22, 17, 8, 13, 19, 15, 9, 11, 12, 11, 9, 10, 10, 10, 12, 9, 5, 8, 16, 12, 27, 18, 23, 27, 12, 12, 18, 18, 22, 10, 10, 5, 6, 12, 11, 11, 12, 35, 15, 10, 40, 26, 15, 27, 8, 16, 10, 8, 7, 16, 23, 27, 11, 10, 20, 16, 13, 12, 11, 19, 8, 12, 12, 10, 22, 12, 10, 8, 10, 12, 9, 6, 6, 15, 11, 15, 10, 29, 23, 23, 20, 20, 15, 11, 19, 9, 12, 10, 9, 12, 10, 24, 28, 10, 15, 14, 15, 12, 10, 11, 11, 11, 19, 14, 9, 27, 10, 12, 12, 13, 19, 8, 12, 15, 18, 11, 18, 20, 11, 12, 19, 19, 23, 29, 12, 8, 14, 16, 16, 12, 10, 11, 11, 10, 11, 12, 11, 15, 12, 13, 11, 13, 19, 9, 24, 12, 13, 12, 12, 12, 9, 10, 11, 12, 18, 29, 31, 37, 19, 18, 12, 12, 9, 10, 12, 17, 15, 18, 9, 38, 12, 21, 9, 14, 14, 9, 15, 9, 9, 12, 8, 10, 10, 8, 16, 13, 14, 13, 8, 10, 12, 14, 11, 19, 11, 15, 27, 18, 12, 23, 32, 24, 12, 14, 9, 10, 12, 12, 12, 19, 10, 11, 12, 12, 19, 25, 21, 19, 21, 23, 24, 10, 11, 8, 8, 14, 14, 21, 9, 13, 14, 12, 9, 17, 23, 19, 24, 23, 10, 18, 19, 11, 10, 24, 10, 8, 14, 20, 19, 27, 10, 10, 19, 27, 11, 31, 10, 16, 27, 13, 23, 11, 19, 10, 8, 10, 13, 8, 14, 17, 17, 9, 13, 14, 14, 20, 15, 12, 16, 9, 17, 12, 8, 16, 10, 10, 9, 11, 10, 8, 7, 9, 18, 9, 8, 8, 10, 8, 10, 9, 12, 17, 23, 8, 28, 10, 12, 14, 20, 8, 8, 16, 8, 8, 14, 11, 8, 8, 10, 10, 8, 20, 10, 21, 9, 14, 13, 16, 9, 21, 17, 26, 19, 13, 16, 10, 10, 12, 12, 19, 8, 10, 18, 13, 30, 6, 9, 23, 6, 16, 6, 12, 8, 13, 5, 5)
    s = drosophila[[1]]
    s@data$PCON.2 = q
    trims = trim.mott(s)
    expect_equal(trims$start, 0)
    expect_equal(trims$finish, 0)

})