tests/testthat/test-download_ccp_crap.R

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

test_that("check_uniprot_release() works", {
  expect_true(grepl("[0-9]{4}_[0-9]{2}", check_uniprot_release()))
})

test_that("sub_crap() works", {
  expect_equal(sub_crap("|text|"), "|cRAP001|text|")
  expect_equal(sub_crap("|text|", 77), "|cRAP077|text|")
  expect_equal(sub_crap("|text|", 111, 4), "|cRAP0111|text|")
})

# test_that("download_ccp_crap() works", {
#   # create self cleaning tempfile
#   withr::with_tempfile("tf", {
#
#     # download CCP cRAP fasta sequences from UniProt
#     download_ccp_crap(
#       file = tf,
#       is_crap = TRUE,
#       overwrite = FALSE,
#       verbose = TRUE
#     )
#
#     # load fasta into memory
#     target <- Biostrings::readAAStringSet(filepath = tf)
#
#     # Use expect_snapshot_output(str()) rather than expect_snapshot_file(), which
#     # should hopefully be more robust to small changes in UniProt headers or
#     # sequences that can occur over time.
#
#     # compare just downloaded cRAP to snapshot
#     expect_snapshot_output(str(target@ranges))
#   })
# })