tests/testthat/test_3_name_conversions.R

In imkeller/immunotation: Tools for working with diverse immune genes

context("P and G groups")

test_that("get_G_group() and get_P_group() return error when arguments not adequate", {
    expect_error(get_G_group("foo"))
    expect_error(get_P_group("foo"))
    expect_error(get_G_group("*"))
    expect_error(get_P_group("*"))
    expect_error(get_G_group("HLA-A*"))
    expect_error(get_P_group("HLA-A*"))
})

test_that("get_G_group() and get_P_group() return expected results", {
    # this should return something else
    expect_equal(get_G_group("HLA-A*01:01:01:01")[[1]], "A*01:01:01G")
    expect_equal(get_G_group("A*01:01:01:01")[[1]], 
                 get_G_group("HLA-A*01:01:01:01")[[1]])
    expect_equal(get_G_group("DQB1*02:02:01")[[1]], 
                 get_G_group("HLA-DQB1*02:02:01")[[1]])
    expect_equal(get_P_group("A*01:01:01:01")[[1]], "A*01:01P")
    expect_equal(get_P_group("A*01:01:01:01")[[1]], 
                 get_P_group("HLA-A*01:01:01:01")[[1]])
    expect_equal(get_P_group("DQB1*02:02:01")[[1]], 
                 
                 get_P_group("HLA-DQB1*02:02:01")[[1]])
})


context("Get MHC input from allele list")

test_that("get_mhcpan_input() returns error when arguments not adequate", {
    expect_error(get_mhcpan_input())
    expect_error(get_mhcpan_input(allele_list = "", mhc_class = "MHC-I"))
    expect_error(get_mhcpan_input(mhc_class = "MHC-I"))
    expect_error(get_mhcpan_input(allele_list = "A*01:01", mhc_class = "foo"))
    expect_error(get_mhcpan_input(allele_list = "foo", mhc_class = "MHC-I"))
})

test_that("get_mhcpan_input() returns error when alleles not in the list", {
    expect_error(get_mhcpan_input("A*01", mhc_class = "MHC-I"))
    expect_error(get_mhcpan_input("DRB1*01", mhc_class = "MHC-II"))
    expect_error(get_mhcpan_input("HLA-DRB1*01", mhc_class = "MHC-II"))
    expect_error(get_mhcpan_input("A*01:01", mhc_class = "MHC-II"))
    expect_error(get_mhcpan_input("DRB1*01:01", mhc_class = "MHC-I"))
})

test_that("get_mhcpan_input() returns expected results", {
    # MHC I
    expect_equal(get_mhcpan_input("A*01:01", mhc_class = "MHC-I"), "HLA-A01:01")
    expect_equal(get_mhcpan_input("A*01:01:01:01", mhc_class = "MHC-I"), 
                 "HLA-A01:01")
    expect_equal(get_mhcpan_input("HLA-A*01:01", mhc_class = "MHC-I"), 
                 "HLA-A01:01")
    # MHC II
    expect_equal(get_mhcpan_input("DRB1*01:01", mhc_class = "MHC-II"), 
                 "DRB1_0101")
    expect_equal(get_mhcpan_input(allele_list = "HLA-DRB1*01:01", 
                                  mhc_class = "MHC-II"), "DRB1_0101")
    expect_equal(length(get_mhcpan_input(allele_list = c("DPA1*01:03:01", 
                                                         "DPB1*14:01:01"), 
                                         mhc_class = "MHC-II")), 1)
})


context("MAC conversion")

test_that("encode_MAC() returns error when arguments not adequate", {
    expect_error(encode_MAC())
    expect_equal(encode_MAC(""), "glstring is empty")
    expect_error(encode_MAC("A*01:01", "A*01:02"))
    
    # this should return an error warning
    expect_equal(encode_MAC("foo"), 
                 "No Locus for allele: foo")
})

test_that("encode_MAC() returns expected results", {
    expect_equal(encode_MAC("A*01:01"), "A*01:01")
    expect_equal(encode_MAC(c("A*01:01", "A*01:02")), "A*01:AB")
})

test_that("decode_MAC() returns error when arguments not adequate", {
    expect_error(decode_MAC())
    expect_equal(decode_MAC(""), "Empty allele designation")
    expect_error(decode_MAC("A*01:01", "A*01:02"))
    
    # this should return an error warning
    expect_equal(decode_MAC("foo"), "No asterisk in allele designation: 'foo'")
})

test_that("decode_MAC() returns expected results", {
    expect_is(decode_MAC("A*01:01"), "character")
    expect_is(decode_MAC("A*01:AB"), "character")
})