tests/testthat/test-parse_fasta_headers.R

In currocam/utilsHMMER: HMMERutils

test_that("local (i.e. no database reference) works", {
    parse_fasta_headers(
        c(
            "lcl|123",
            "lcl|hmm271 description"
        )
    ) %>%
        expect_equal(
            c(
                "123",
                "hmm271"
            )
        )
})
test_that("GenInfo backbone seqid  works", {
    parse_fasta_headers(
        c(
            "bbs|123 ",
            "bbs|123 "
        )
    ) %>%
        expect_equal(
            c(
                "123",
                "123"
            )
        )
})
test_that("GenInfo backbone moltype   works", {
    parse_fasta_headers(
        c(
            "bbm|123",
            "bbm|123 "
        )
    ) %>%
        expect_equal(
            c(
                "123",
                "123"
            )
        )
})
test_that("GenInfo import ID  works", {
    parse_fasta_headers(
        c(
            "gim|123",
            "gim|123"
        )
    ) %>%
        expect_equal(
            c(
                "123",
                "123"
            )
        )
})
test_that("GenBank works", {
    parse_fasta_headers(
        c(
            "gb|M73307|AGMA13GT",
            "gb|M73307|AGMA13GT"
        )
    ) %>%
        expect_equal(
            c(
                "M73307",
                "M73307"
            )
        )
})
test_that("EMBL works", {
    parse_fasta_headers(
        c(
            "emb|CAM43271.1|",
            "emb|CAM43271.1|"
        )
    ) %>%
        expect_equal(
            c(
                "CAM43271.1",
                "CAM43271.1"
            )
        )
})
test_that("PIR works", {
    parse_fasta_headers(
        c(
            "pir||G36364",
            "pir||G36364"
        )
    ) %>%
        expect_equal(
            c(
                "G36364",
                "G36364"
            )
        )
})
test_that("SWISS-PROT works", {
    parse_fasta_headers(
        c(
            "sp|P01013|OVAX_CHICK",
            "sp|P01013|OVAX_CHICK description"
        )
    ) %>%
        expect_equal(
            c(
                "OVAX_CHICK",
                "OVAX_CHICK"
            )
        )
})
test_that("patent works", {
    parse_fasta_headers(
        c(
            "pat|US|RE33188|1",
            "pat|US|RE33188|1"
        )
    ) %>%
        expect_equal(
            c(
                "RE33188",
                "RE33188"
            )
        )
})
test_that("pre-grant patent  works", {
    parse_fasta_headers(
        c(
            "pgp|EP|0238993|7",
            "pgp|EP|0238993|7"
        )
    ) %>%
        expect_equal(
            c(
                "0238993",
                "0238993"
            )
        )
})
test_that("RefSeq works", {
    parse_fasta_headers(
        c(
            "ref|NM_010450.1|",
            "ref|NM_010450.1|"
        )
    ) %>%
        expect_equal(
            c(
                "NM_010450.1",
                "NM_010450.1"
            )
        )
})
test_that("general database referenceworks ", {
    parse_fasta_headers(
        c(
            "gnl|taxon|9606",
            "gnl|PID|e1632"
        )
    ) %>%
        expect_equal(
            c(
                "9606",
                "e1632"
            )
        )
})
test_that("GenInfo integrated database  works", {
    parse_fasta_headers(
        c(
            "gi|21434723",
            "gi|21434723"
        )
    ) %>%
        expect_equal(
            c(
                "21434723",
                "21434723"
            )
        )
})
test_that("DDBJworks", {
    parse_fasta_headers(
        c(
            "dbj|BAC85684.1|",
            "dbj|BAC85684.1|"
        )
    ) %>%
        expect_equal(
            c(
                "BAC85684.1",
                "BAC85684.1"
            )
        )
})
test_that("PRF works", {
    parse_fasta_headers(
        c(
            "prf||0806162C",
            " prf||0806162C"
        )
    ) %>%
        expect_equal(
            c(
                "0806162C",
                "0806162C"
            )
        )
})
test_that("pdb works", {
    parse_fasta_headers(
        c(
            "pdb|1I4L|D",
            "pdb|1I4L|D"
        )
    ) %>%
        expect_equal(
            c(
                "1I4L_D",
                "1I4L_D"
            )
        )
})
test_that("third-party GenBank works", {
    parse_fasta_headers(
        c(
            "tpg|BK003456|",
            "tpg|BK003456|"
        )
    ) %>%
        expect_equal(
            c(
                "BK003456",
                "BK003456"
            )
        )
})
test_that("third-party EMBL works", {
    parse_fasta_headers(
        c(
            "tpe|BN000123|",
            "tpe|BN000123|"
        )
    ) %>%
        expect_equal(
            c(
                "BN000123",
                "BN000123"
            )
        )
})
test_that("third-party DDBJ works", {
    parse_fasta_headers(
        c(
            "tpd|FAA00017|",
            "tpd|FAA00017|"
        )
    ) %>%
        expect_equal(
            c(
                "FAA00017",
                "FAA00017"
            )
        )
})
test_that("TrEMBL works", {
    parse_fasta_headers(
        c(
            "tr|Q90RT2|Q90RT2_9HIV1",
            "tr|Q90RT2|Q90RT2_9HIV1"
        )
    ) %>%
        expect_equal(
            c(
                "Q90RT2_9HIV1",
                "Q90RT2_9HIV1"
            )
        )
})