tests/testthat/test-create_consensus_topology_conservation.R

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

# test_that("use, simple data, pureseqtmr", {
#
#   if (!pureseqtmr::is_pureseqtm_installed()) return()
#
#   protein_sequences <- c(
#     "IMPRESSIVELYFLIFAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#      "MPRESSIVELYFLIAAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#      "IMPRESSIVELYFLMTAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIF",
#     "IMPRESSIVELYFLIIAWAYANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#     "IMPRESSIVELYFLILAWAYFANSWALKWEETMARKETTRIVIALLYNAILIDENTIFY",
#     "IMPRESSIVELYFLIYAWAYFANSWALKSWEETMARKETRIVIALLYNAILIDENTIFY"
#   )
#   library(msa)
#   t <- create_consensus_topology_conservation(
#     protein_sequences,
#     topology_prediction_tool = "pureseqtmr",
#     msa_method = "ClustalOmega",
#     msa_subst_matrix = "BLOSUM80"
#   )
#   expect_true(tibble::is_tibble(t))
#   expect_equal(60, nrow(t))
# })
#
# test_that("use, simple data, tmhmm", {
#
#   if (!tmhmm::is_tmhmm_installed()) return()
#   skip("https://github.com/richelbilderbeek/bbbq_article/issues/74")
#
#   # This is the problem, which will be a tmhmm test
#   consensus <- "IMPRESSIVELYFLI?AWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY"
#   #                            ^
#   #                            |
#   #                            +----- Possible cause of the problem
#   #
#   topology <- tmhmm::run_tmhmm_on_sequence(consensus) # Gives error
#
#   # This is the actual BBBQ test:
#
#
#   protein_sequences <- c(
#     "IMPRESSIVELYFLIFAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#      "MPRESSIVELYFLIAAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#      "IMPRESSIVELYFLMTAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIF",
#     "IMPRESSIVELYFLIIAWAYANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#     "IMPRESSIVELYFLILAWAYFANSWALKWEETMARKETTRIVIALLYNAILIDENTIFY",
#     "IMPRESSIVELYFLIYAWAYFANSWALKSWEETMARKETRIVIALLYNAILIDENTIFY"
#   )
#   t <- create_consensus_topology_conservation(
#     protein_sequences,
#     topology_prediction_tool = "tmhmm",
#     msa_method = "ClustalOmega",
#     msa_subst_matrix = "BLOSUM80"
#   )
#   expect_true(tibble::is_tibble(t))
#   expect_equal(60, nrow(t))
# })
#
# test_that("use, ClustalOmega, simple data", {
#
#   if (!pureseqtmr::is_pureseqtm_installed()) return()
#   protein_sequences <- c(
#     "IMPRESSIVELYFLIFAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#      "MPRESSIVELYFLIAAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#      "IMPRESSIVELYFLMTAWAYFANSWALKSWEETMARKETTRIVIALLYNAILIDENTIF",
#     "IMPRESSIVELYFLIIAWAYANSWALKSWEETMARKETTRIVIALLYNAILIDENTIFY",
#     "IMPRESSIVELYFLILAWAYFANSWALKWEETMARKETTRIVIALLYNAILIDENTIFY",
#     "IMPRESSIVELYFLIYAWAYFANSWALKSWEETMARKETRIVIALLYNAILIDENTIFY"
#   )
#
#   t <- create_consensus_topology_conservation(
#     protein_sequences,
#     topology_prediction_tool = "pureseqtmr",
#     msa_method = "ClustalOmega",
#     msa_subst_matrix = "BLOSUM80"
#   )
#   expect_true(tibble::is_tibble(t))
#   expect_equal(60, nrow(t))
# })
#
# test_that("Cannot align sequence with only unknown amino acids", {
#
#   if (!pureseqtmr::is_pureseqtm_installed()) return()
#   # Bugreport at
#   # https://github.com/richelbilderbeek/bbbq_article/issues/104
#
#   protein_sequences <- c(
#     "MYSFVSEETGTLIVNSVLL",
#     "MYSFVSEETGTLIVNSVLL",
#     "XXXXXXXXXXXXXXXXXXX"
#   )
#   expect_error(
#     create_consensus_topology_conservation(
#       protein_sequences,
#       topology_prediction_tool = "pureseqtmr",
#       msa_method = "ClustalOmega",
#       msa_subst_matrix = "BLOSUM80"
#     ),
#     "Cannot align sequence with only unknown amino acids"
#   )
# })
#
# test_that("Can save MSA", {
#
#   if (!pureseqtmr::is_pureseqtm_installed()) return()
#   # https://github.com/richelbilderbeek/bbbq_article/issues/128
#
#   protein_sequences <- c(
#     "MYSFVSEETGTLIVNSVLL",
#     "MYSFVSEETGTLIVNSVL"
#   )
#   msa_filename <- tempfile()
#
#   library(msa)
#   # Cannot expect this to be silent, probably due to libs being loaded
#   create_consensus_topology_conservation(
#     protein_sequences,
#     topology_prediction_tool = "pureseqtmr",
#     msa_method = "ClustalOmega",
#     msa_subst_matrix = "BLOSUM80",
#     msa_filename = msa_filename
#   )
#   expect_true(file.exists(msa_filename))
# })