tests/testthat/test-search_jackhmmer.R

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

test_that("non protein sequences fails", {
  search_jackhmmer("12333333dshjdkasdb") %>%
    expect_error(paste0("`seq` must be a protein sequence.\n",
                        "Characters not belonging to the AA standar ",
                        "alphabet were found."))
  search_jackhmmer(12333333) %>%
    expect_error(paste0("`seq` must be a protein sequence.\n",
                        "Characters not belonging to the AA standar ",
                        "alphabet were found."))
  search_jackhmmer(environment()) %>%
    expect_error()

})

testthat::skip_if_offline()
testthat::skip_on_ci()

test_that("it works with sequence", {
  seq <- "MGPSENDPNLFVA"
  search_jackhmmer(seq) %>%
    expect_error(NA)
  search_jackhmmer(c(seq, seq),
                 db = c("swissprot", "pdb"),alignment = TRUE) %>%
    expect_error(NA)
})


test_that("it works with aln", {
  aln <- Biostrings::readAAMultipleAlignment("alignment.aln", "stockholm")
  search_jackhmmer(alns = c(aln, aln),
                   db = c("swissprot", "pdb"), alignment = TRUE) %>%
    expect_error(NA)
})