tests/testthat/test-pairwise_alignment_sequence_identity.R

In currocam/taxa2hmmer: Get more out of homologous sequence search with HMMER

test_that("pairwise_alignment autoplot works", {
  seqs <- Biostrings::readAAStringSet("fasta.fa")
  ann_seqs <- rep(c("cat", "dog", "koala"), c(3, 5, 3))
  pairwise.object <- pairwise_alignment_sequence_identity(seqs)
  vdiffr::expect_doppelganger("A pairwise histogram",
                              plot(pairwise.object))
  vdiffr::expect_doppelganger("A pairwise histogram",
                              plot(pairwise.object,
                                   type = "hist",
                                   annotation = ann_seqs))
  vdiffr::expect_doppelganger("A pairwise heatmap",
                              plot(pairwise.object, type = "heatmap"))
    vdiffr::expect_doppelganger("A pairwise annotated",
                              plot(pairwise.object, type = "heatmap",
                                   annotation = ann_seqs))
  plot(pairwise.object, type = "heatmap", annotation = c("factor")) %>%
    testthat::expect_warning()
})

test_that("pairwise_alignment works", {
  seqs <- Biostrings::readAAStringSet("fasta.fa")
  pairwise_alignment_sequence_identity(seqs) %>%
    dplyr::pull("percentage.sequence.identity") %>%
    expect_snapshot_value(style = "deparse")
})

testthat::skip_on_ci()
test_that("pairwise_alignment works with furrr", {
  Biostrings::readAAStringSet("fasta.fa")%>%
    pairwise_alignment_sequence_identity(
      allow_parallelization = "multisession"
      ) %>%
    dplyr::pull("percentage.sequence.identity") %>%
    expect_snapshot_value(style = "deparse")
})

test_that("pairwise_alignment works with local and PID2", {
  fasta <- Biostrings::readAAStringSet("fasta.fa")
  fasta[1:4] %>%
    pairwise_alignment_sequence_identity(
      aln_type = "local",
      pid_type = "PID2",
      allow_parallelization = "multisession"
    )%>%
    dplyr::pull("percentage.sequence.identity") %>%
    expect_snapshot_value(style = "deparse")
})

test_that("pairwise_alignment works with overlap and PID3", {
  fasta <- Biostrings::readAAStringSet("fasta.fa")
  fasta[1:4] %>%
    pairwise_alignment_sequence_identity(
      aln_type = "overlap",
      pid_type = "PID3",
      allow_parallelization = "multisession"
    )%>%
    dplyr::pull("percentage.sequence.identity") %>%
    expect_snapshot_value(style = "deparse")
})

test_that("pairwise_alignment works with local and PID4", {
  fasta <- Biostrings::readAAStringSet("fasta.fa")
  fasta[1:4] %>%
    pairwise_alignment_sequence_identity(
      aln_type = "local",
      pid_type = "PID4",
      allow_parallelization = "multisession"
    )%>%
    dplyr::pull("percentage.sequence.identity") %>%
    expect_snapshot_value(style = "deparse")
})