tests/testthat/test_Proteins-class.R

In Pbase: Manipulating and exploring protein and proteomics data

context("Proteins-class")

test_that("fasta constructor", {
  expect_error(Proteins("foobar.txt"),
               "The file.s. .*foobar.txt.* do.es. not exist!")
               #paste0("The file(s) ", sQuote("foobar.txt"),
               #       " do(es) not exist!"))

  f <- file.path(system.file("extdata", package = "Pbase"),
                 "01_test_database.fasta")
  aa <- AAStringSet(c(
  "td|P1|P1_TEST protein 1, length 10 OS=machina arithmetica GN=g1 PE=1 SV=1" =
    "AKAKBKCKDE",
  "td|P2|P2_TEST protein 2, length 5 OS=machina arithmetica GN=g2 PE=1 SV=1" =
    "FKGHD",
  "td|P3|P3_TEST protein 3, length 15 OS=machina arithmetica GN=g3 PE=1 SV=1" =
    "JKKLMKNKDOPQRST"))
  names(aa) <- c("P1", "P2", "P3")

  p <- Proteins(f)
  p2 <- p
  p2@aa <- p@aa[1:2]
  p2@aa@elementMetadata <- p@aa@elementMetadata[1:2,, drop=FALSE]

  expect_identical(length(p), 3L)
  expect_identical(nrow(acols(p)), 3L)
  expect_identical(as.integer(acols(p)$Filename), rep(1L, 3L))
  expect_identical(basename(levels(acols(p)$Filename)),
                   "01_test_database.fasta")

  expect_identical(seqnames(p), c("P1", "P2", "P3"))

  expect_identical(as.character(p@aa), as.character(aa))
  expect_identical(as.character(p[[1]]), as.character(aa[[1]]))
  expect_identical(as.character(p[1:2]@aa), as.character(p2@aa))

  expect_identical(acols(p[1:2]), acols(p2))

  expect_true(is.character(metadata(p)$created))
  expect_identical(nchar(metadata(p)$created,), 24L)
  expect_true(grepl(paste0("[A-z]{3} [A-z]{3} +[0-9]{1,2} ",
                           "[0-9]{2}:[0-9]{2}:[0-9]{2} [0-9]{4}"),
                    metadata(p)$created))
})