tests/testthat/test-HMMER.R

In currocam/utilsHMMER: HMMERutils

testthat::skip_on_ci()
httptest::with_mock_api({
    testthat::test_that("mock phmmer works", {
        search_in_hmmer(
            algorithm = "phmmer",
            seqdb = "pdb",
            seq = ">Seq\nKLRVLGYHNGEWCEAQTKNGQGWVPSNYITPVNSLENSIDKHSWYHGPVSRNAAE"
        ) %>%
            testthat::expect_snapshot()
    })
})

httptest::with_mock_api({
    testthat::test_that("mock hmmscan works", {
        search_in_hmmer(
            algorithm = "hmmscan",
            hmmdb = "pfam",
            seq = ">Seq\nKLRVLGYHNGEWCEAQTKNGQGWVPSNYITPVNSLENSIDKHSWYHGPVSRNAAE"
        ) %>%
            testthat::expect_snapshot()
    })
})

httptest::with_mock_api({
    testthat::test_that("mock hmmsearch works", {
        aln <- Biostrings::readAAMultipleAlignment("alignment.fasta") %>%
            Biostrings::unmasked() %>%
            format_AAStringSet_into_hmmer_string()
        search_in_hmmer(
            algorithm = "hmmsearch",
            seqdb = "swissprot",
            seq = aln
        ) %>%
            testthat::expect_snapshot()
    })
})

httptest::with_mock_api({
    testthat::test_that("mock phmmer with wrong input fails", {
        search_in_hmmer(
            algorithm = "phmmer",
            hmmdb = "pfam",
            seq = ">Seq\nKLRVLGYHNGEWCEAQTKNGQGWVPSNYITPVNSLENSIDKHSWYHGPVSRNAAE"
        ) %>%
            testthat::expect_snapshot()
    })
})

httptest::with_mock_api({
    testthat::test_that("mock hmmscan with wrong input fails", {
        search_in_hmmer(
            algorithm = "hmmscan",
            seqdb = "pdb",
            seq = ">Seq\nKLRVLGYHNGEWCEAQTKNGQGWVPSNYITPVNSLENSIDKHSWYHGPVSRNAAE"
        ) %>%
            testthat::expect_snapshot()
    })
})

httptest::with_mock_api({
    testthat::test_that("mock hmmsearch with wrong input fails", {
        search_in_hmmer(
            algorithm = "hmmsearch",
            seqdb = "pdb",
            seq = ">Seq\nKLRVLGYHNGEWCEAQTKNGQGWVPSNYITPVNSLENSIDKHSWYHGPVSRNAAE"
        ) %>%
            testthat::expect_snapshot()
    })
})