tests/testthat/test-translate.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

## translate.R exports the following:
## - translate (DNAString, RNAString, DNAStringSet, RNAStringSet,
##                                MaskedDNAString, MaskedRNAString, Default)
## - codons (DNAString, RNAString, MaskedDNAString, MaskedRNAString, Default)

d <- DNAString(paste(names(GENETIC_CODE), collapse=""))
r <- as(d, "RNAString")
a <- AAString(paste(GENETIC_CODE, collapse=""))

test_that("translate works properly for all dna,rna", {
    ## basic conversion
    expect_identical(translate(d), a)
    expect_identical(translate(r), a)

    dd <- DNAStringSet(list(d,d))
    rr <- RNAStringSet(list(r,r))
    aa <- AAStringSet(list(a,a))
    expect_identical(translate(dd) == aa, c(TRUE, TRUE))
    expect_identical(translate(rr) == aa, c(TRUE, TRUE))

    ## errors
    expect_error(translate(BString()), "unable to find an inherited method")
    expect_error(translate(AAString()), "unable to find an inherited method")
    expect_error(translate("ATG"), "unable to find an inherited method")

    alt_gen_code <- GENETIC_CODE
    alt_gen_code[] <- rep(c("A", "B"), each=32L)
    alt_a <- AAString(paste(rep(c("A", "B"), each=32L), collapse=""))
    alt_aa <- AAStringSet(list(alt_a, alt_a))
    expect_identical(translate(d, genetic.code=alt_gen_code), alt_a)
    expect_identical(translate(r, genetic.code=alt_gen_code), alt_a)
    expect_identical(translate(dd, genetic.code=alt_gen_code) == alt_aa,
                     c(TRUE, TRUE))
    expect_identical(translate(rr, genetic.code=alt_gen_code) == alt_aa,
                     c(TRUE, TRUE))

    ## fault paths
    expect_error(translate(d, genetic.code=character(0L)),
        "'genetic.code' must have the same names as predefined constant GENETIC_CODE", fixed=TRUE)
    expect_error(translate(d, genetic.code=GENETIC_CODE[seq_len(10L)]),
        "'genetic.code' must have the same names as predefined constant GENETIC_CODE", fixed=TRUE)
    alt_gen_code[] <- ""
    expect_error(translate(d, genetic.code=alt_gen_code),
        "'genetic.code' must contain 1-letter strings", fixed=TRUE)

    ## this is promoted to an error with this test case
    alt_gen_code[] <- "/"
    expect_error(translate(d, genetic.code=alt_gen_code),
        "some codons in 'genetic.code' are mapped to letters not in the Amino Acid\n  alphabet", fixed=TRUE)

    ## alt_init_codon args
    ## error message could be more informative here
    error_msg <- "'genetic.code' must have an \"alt_init_codons\" attribute"
    alt_gen_code <- GENETIC_CODE
    attr(alt_gen_code, "alt_init_codons")[] <- c("BLAH", "NOTANAMINOACID")
    expect_error(translate(d, genetic.code=alt_gen_code), error_msg, fixed=TRUE)
    attr(alt_gen_code, "alt_init_codons")[] <- c("AAA", "AAA")
    expect_error(translate(d, genetic.code=alt_gen_code), error_msg, fixed=TRUE)
    attr(alt_gen_code, "alt_init_codons")[] <- c(NA_character_, "AAA")
    expect_error(translate(d, genetic.code=alt_gen_code), error_msg, fixed=TRUE)
    attr(alt_gen_code, "alt_init_codons")[] <- c(1,2)
    expect_error(translate(d, genetic.code=alt_gen_code), error_msg, fixed=TRUE)
    attr(alt_gen_code, "alt_init_codons") <- NULL
    expect_error(translate(d, genetic.code=alt_gen_code), error_msg, fixed=TRUE)

    ## alternate init codons
    dna1 <- DNAString("TTGATATGGCCCTTATAA")
    expect_identical(translate(dna1), AAString("MIWPL*"))
    expect_identical(translate(dna1, no.init.codon=TRUE), AAString("LIWPL*"))
    rna1 <- as(dna1, "RNAString")
    expect_identical(translate(rna1), AAString("MIWPL*"))
    expect_identical(translate(rna1, no.init.codon=TRUE), AAString("LIWPL*"))

    ## fuzzy codons
    dna1 <- DNAString("TTYTTTTTC")
    expect_error(translate(dna1), "not a base at pos 3")
    expect_identical(translate(dna1, if.fuzzy.codon="solve"), AAString("FFF"))
    expect_identical(translate(dna1, if.fuzzy.codon="X"), AAString("XFF"))
    expect_identical(translate(dna1, if.fuzzy.codon="error.if.X"),
                     AAString("XFF"))

    dna2 <- DNAString("TTNTTYTTC")
    expect_identical(translate(dna2, if.fuzzy.codon="solve"), AAString("XFF"))
    expect_identical(translate(dna2, if.fuzzy.codon="X"), AAString("XXF"))
    expect_error(translate(dna2, if.fuzzy.codon="error.if.X"),
                 "ambiguous fuzzy codon starting at pos 1")

    expect_error(translate(dna2, if.fuzzy.codon="blahblahblaherror"),
                 "'arg' should be one of ", fixed=TRUE)
})

test_that("translate, codons work properly for masked strings and string sets", {
    mask0 <- Mask(mask.width=nchar(d), start=c(4,10), width=3)
    mask1 <- Mask(mask.width=nchar(d), start=c(4,10), width=4)
    mask2 <- Mask(mask.width=nchar(d), start=1, width=5)

    dm <- d
    rm <- r
    masks(dm) <- masks(rm) <- mask0

    m_a <- AAString(paste(GENETIC_CODE[-c(2,4)], collapse=""))
    expect_identical(translate(dm), m_a)
    expect_identical(translate(rm), m_a)

    codon_views_d <- codons(dm)
    codon_views_r <- codons(rm)
    svec <- c(1L, 7L, seq(13L,nchar(d),3L))
    expect_identical(start(codon_views_d), svec)
    expect_identical(start(codon_views_r), svec)
    expect_identical(end(codon_views_d), svec+2L)
    expect_identical(end(codon_views_r), svec+2L)

    masks(d) <- mask1
    expect_warning(translate(d), "last base was ignored")

})

test_that("codon function works properly", {
    expect_identical(codons(d), Views(d, start=seq(1,nchar(d),3), width=3))
    expect_identical(codons(r), Views(r, start=seq(1,nchar(d),3), width=3))

    expect_warning(codons(DNAString("AT")),
                   "the number of nucleotides in 'x' is not a multiple of 3")
    expect_warning(codons(DNAString("ATATA")),
                   "the number of nucleotides in 'x' is not a multiple of 3")
    expect_warning(codons(RNAString("AU")),
                   "the number of nucleotides in 'x' is not a multiple of 3")
    expect_warning(codons(RNAString("AUAUA")),
                   "the number of nucleotides in 'x' is not a multiple of 3")

    expect_error(codons(AAString()),
                 "unable to find an inherited method for function")
    expect_error(codons(BString()),
                 "unable to find an inherited method for function")
    expect_error(codons("ATG"),
                 "unable to find an inherited method for function")
})