tests/testthat/test-MSD.R

In ipb-halle/GoldenMutagenesis: A tool to calculate and validate primers for Golden Gate Cloning

context("Multiple Site Saturation Mutagenesis")

#load("../../data/MSD_BsaI_setup_lv2.RData")
load(file.path(system.file("data", package="GoldenMutagenesis"), "MSD_BsaI_setup_lv2.RData"))
primer_test<-mutate_msd(input_sequence = input_sequence, replacements = mutations, restriction_enzyme = recognition_site_bsai)
#load("../../data/MSD_BsaI_result_lv2.RData")
load(file.path(system.file("data", package="GoldenMutagenesis"), "MSD_BsaI_result_lv2.RData"))

test_that("Known primers are calculated correctly (MSD)", {
  expect_that(primer_test, is_identical_to(primers))
})

primer_test_lc<-mutate_msd(input_sequence = str_to_lower(input_sequence), replacements = mutations, restriction_enzyme = str_to_lower(recognition_site_bsai))

test_that("Known primers are calculated correctly (MSD) for lowercase sequences", {
  expect_that(primer_test_lc, is_identical_to(primer_test))
})

load("MSD_BsaI_result_lv0.RData")
primer_test_lvl0<-primer_add_level(primers,  prefix="TT", restriction_enzyme="GAAGAC", suffix="AA", vector=c("CTCA", "CTCG"))

load("MSD_5_265.RData")
load("MSD_265.RData")

test_that("Start and End Positions are calculated correctly", {
  expect_that(mutate_msd(input_sequence = input_sequence, replacements = c(5, 265), restriction_enzyme = recognition_site_bsai), is_identical_to(primers_5_265))
  expect_that(mutate_msd(input_sequence = input_sequence, replacements = c(265), restriction_enzyme = recognition_site_bsai), is_identical_to(primers_265))
})

test_that("Adding level0 to a set of primers works", {
  expect_that(primer_test_lvl0, is_identical_to(primers_lvl0))
})

primer_test_lvl0_lc<-primer_add_level(primers,  prefix=str_to_lower("TT"), restriction_enzyme=str_to_lower("GAAGAC"), suffix=str_to_lower("AA"), vector=str_to_lower(c("CTCA", "CTCG")))

test_that("Adding level0 to a set of primers works for lowercase sequences", {
  expect_that(primer_test_lvl0, is_identical_to(primer_test_lvl0_lc))
})

rm(primers)
load("MSD_issue_27.RData")
mutations<-c(232,234)
primer_issue_27<-primers<-mutate_msd(input_sequence, prefix="TT" ,restriction_enzyme=recognition_site_bsai, suffix="A", vector=c("AATG", "AAGC"), replacements=mutations, replacement_range=5, binding_min_length=4 ,binding_max_length = 9, target_temp=60, fragment_min_size=60 )
test_that("Checking for bug of issue #27", {
  expect_that(primer_issue_27, is_identical_to(primers))
})
rm(primers)