tests/testthat/test-extract_from_HMMER_data_tbl.R

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

test_that("works when phmmer", {
  read_hmmer_from_xml(
    rep("phmmer_example.xml", 3), rep("phmmer_example.fa", 3)) %>%
    extract_from_HMMER_data_tbl() %>%
    testthat::expect_error(NA)
  read_hmmer_from_xml(
    rep("phmmer_example.xml", 1), rep("phmmer_example.fa", 1)) %>%
    extract_from_HMMER_data_tbl(id_column = "unique",
                                remove_redundancy = TRUE,
                                annotate_taxonomic = "local") %>%
    write.csv("phmmer_tidy_tbl.csv")
    testthat::expect_snapshot_file("phmmer_tidy_tbl.csv")
})
test_that("works when phmmer", {
  read_hmmer_from_xml("phmmer_example.xml",
                      "phmmer_example.fa",
                      "phmmer_example.afa") %>%
    extract_from_HMMER_data_tbl(id_column = "unique",
                                remove_redundancy = TRUE,
                                annotate_taxonomic = "local") %>%
    write.csv("phmmer_tidy_tbl_afa.csv")
    testthat::expect_snapshot_file("phmmer_tidy_tbl_afa.csv")
  })

test_that("works when properties", {
  suppressWarnings({
    read_hmmer_from_xml("phmmer_example.xml",
                        "phmmer_example.fa") %>%
      extract_from_HMMER_data_tbl(id_column = "unique",
                                  remove_redundancy = TRUE,
                                  annotate_taxonomic = "local",
                                  calculate_physicochemical_properties = TRUE) %>%
      write.csv("tidy_tbl_properties.csv")
  })
  testthat::expect_snapshot_file("tidy_tbl_properties.csv")
})


test_that("filtering works",{
  read_hmmer_from_xml(
    rep("phmmer_example.xml", 1), rep("phmmer_example.fa", 1)) %>%
    extract_from_HMMER_data_tbl(id_column = "unique",
                                remove_redundancy = TRUE,
                                annotate_taxonomic = "local",
                                evalue = 0.001) %>%
    write.csv("phmmer_tidy_tbl_filtered.csv")
  testthat::expect_snapshot_file("phmmer_tidy_tbl_filtered.csv")
})

test_that("summary works",{
  read_hmmer_from_xml(
    rep("phmmer_example.xml", 3), rep("phmmer_example.fa", 3)) %>%
    extract_from_HMMER_data_tbl() %>%
    summary() %>%
    expect_snapshot_output()
})

test_that("plot works",{
  temp <- read_hmmer_from_xml(
    rep("phmmer_example.xml", 3), rep("phmmer_example.fa", 3)) %>%
    extract_from_HMMER_data_tbl()
  vdiffr::expect_doppelganger("A sig. geom_segment",
      plot(temp))
  vdiffr::expect_doppelganger("A sig. geom_segment",
                              plot(temp, threshold = 0.01))
})