inst/unitTests/test_AlignedRead.R

In ShortRead: FASTQ input and manipulation

sp <- SolexaPath(system.file("extdata", package="ShortRead"))
aln <- readAligned(sp, "s_2_export.txt")

.checkAlignedRead_identical<- function(obs, exp)
    ## can't compare external pointers
{
    checkIdentical(as.character(sread(obs)),
                   as.character(sread(exp)))
    checkIdentical(as.character(quality(quality(obs))),
                   as.character(quality(quality(exp))))
    checkIdentical(as.character(id(obs)), as.character(id(exp)))
    checkIdentical(chromosome(obs), chromosome(exp))
    checkIdentical(strand(obs), strand(exp))
    checkIdentical(alignQuality(obs), alignQuality(exp))
    checkIdentical(alignData(obs), alignData(exp))
}

test_AlignedRead_Bowtie <- function() {
    src <- system.file("extdata", "bowtie", package="ShortRead")
    df <- read.table(file.path(src, "s_1_aligned_bowtie.txt"),
                     fill=TRUE, quote="", sep="\t")
    aln <- readAligned(src, "^s_1_aligned_bowtie.txt$", "Bowtie")
    checkIdentical(nrow(df), length(aln))
    checkIdentical(as.character(df[[2]]), as.character(strand(aln)))
    checkIdentical(as.character(df[[3]]), as.character(chromosome(aln)))
    checkIdentical(df[[4]]+1L, position(aln))
    idx <- strand(aln)=="-"
    s1 <- as.character(df[[5]])
    s1[idx] <- as.character(reverseComplement(DNAStringSet(s1[idx])))
    checkIdentical(s1, as.character(sread(aln)))
    q1 <- as.character(df[[6]])
    q1[idx] <- as.character(reverse(BStringSet(q1[idx])))
    checkIdentical(q1, as.character(quality(quality(aln))))
    checkIdentical(as.character(df[[8]]),
                   as.character(alignData(aln)[["mismatch"]]))
}

test_AlignedRead_SOAP <- function() {
    fl <- "soap.txt"
    src <- system.file("unitTests", "cases", package="ShortRead")
    tbl <- read.table(file.path(src, fl), fill=TRUE)
    aln <- readAligned(src, fl, "SOAP")
    checkTrue(validObject(aln))
    checkIdentical(as.character(tbl[[1]]), as.character(id(aln)))
    strand <- as.character(strand(aln))
    checkIdentical(as.character(tbl[[7]]), strand)
    sread <- as.character(sread(aln))
    sread[strand=="-"] <-
        as.character(reverseComplement(sread(aln)))[strand=="-"]
    checkIdentical(as.character(tbl[[2]]), sread)
    qual <- as.character(quality(quality(aln)))
    qual[strand=="-"] <-
        as.character(reverse(quality(quality(aln)))[strand=="-"])
    checkIdentical(as.character(tbl[[3]]), qual)
    checkIdentical(as.character(tbl[[8]]),
                   as.character(chromosome(aln)))
    checkIdentical(tbl[[9]], position(aln))
    checkTrue(all(is.na(quality(alignQuality(aln)))))
    with(pData(alignData(aln)), {
        checkIdentical(tbl[[4]], nEquallyBestHits)
        checkIdentical(as.character(tbl[[5]]),
                       as.character(pairedEnd))
        checkIdentical(tbl[[6]], alignedLength)
        checkIdentical(tbl[[10]], typeOfHit)
        checkIdentical(c("", "G->15A40", "C->2A40\tC->9G40", "", "",
                         "", "", "A->3G40", "", "A->6C40", "T->7A40",
                         "", "", "", "G->9A40", "G->21C40\tA->19T40",
                         "", "A->7G40", "", "", "C->34T40"),
                         hitDetail)
    })
}

test_AlignedRead_readAligned_SolexaExport <- function() {
    obj <- readAligned(analysisPath(sp),
                       pattern="s_2_export.txt", type="SolexaExport")
    checkTrue(validObject(obj))
    checkTrue(is(quality(obj), "SFastqQuality"))
    checkTrue(is(alignQuality(obj), "NumericQuality"))
    checkIdentical(varLabels(alignData(obj)),
                   c("run", "lane", "tile", "x", "y", "filtering", "contig"))
}

test_AlignedRead_readAligned_SolexaExport_filter <- function()
{
    chr <- "chr5.fa"
    filt <- chromosomeFilter(chr)
    obs <- readAligned(sp, "s_2_export.txt", filter=filt)
    exp <- aln[grep(chr, chromosome(aln))]
    .checkAlignedRead_identical(obs, exp)
    obs <- readAligned(analysisPath(sp), "s_2_export.txt",
                       "SolexaExport", filter=filt)
    .checkAlignedRead_identical(obs, exp)
}

test_AlignedRead_readAligned_SolexaExport_withWhat <- function() {
    src <- system.file("unitTests", "cases", package="ShortRead")
    aln <- readAligned(src, "PE_export.txt.gz",
                       type="SolexaExport", withAll=TRUE)
    checkIdentical(400L, length(aln))
    e0 <- c("HWUSI-EAS618_1:1:1:0:1122#AGCACGA/1",
            "HWUSI-EAS618_1:1:1:0:843#ACCACGA/1",
            "HWUSI-EAS618_1:1:1:4:873#ATCACGA/1",
            "HWUSI-EAS618_1:1:1:4:480#ACCACGA/1")
    checkIdentical(e0, as.character(id(aln)[c(1,2, 399, 400)]))
    e1 <- structure(c(41L, 2L, 72L, 4L, 17L, 17L, 5L, 2L, 8L, 70L, 1L,
                      2L, 1L, 1L, 1L, 37L, 1L, 3L, 2L, 1L, 1L, 70L,
                      1L, 1L, 1L, 4L, 31L, 1L, 1L, 1L), .Dim = 30L,
                      .Dimnames = structure(list(c("AACACGA",
                      "AACCCGA", "ACCACGA", "ACCCCGA", "AGACCAA",
                      "AGCACGA", "AGCCCAA", "AGCCCCA", "AGCCCGA",
                      "ATCACGA", "ATCCCCA", "ATCCCGA", "CACCCTC",
                      "CACGACC", "CCCCCGA", "CGACCAA", "CGACCAC",
                      "CGCCCAA", "CGCCCCA", "CTCCCTT", "GCGCCCA",
                      "GGACCAA", "GGACCCA", "GGACNAA", "GGCCCAA",
                      "NNNNNNN", "TGACCAA", "TGCCCTA", "TTCCCTG",
                      "TTCCCTT")), .Names = ""), class = "table")
    checkIdentical(e1, table(alignData(aln)[["multiplexIndex"]]))

    aln0 <- readAligned(src, "PE_export.txt.gz",
                        type="SolexaExport",
                        withId=TRUE, withMultiplexIndex=TRUE)
    checkIdentical(sub("/1$", "", as.character(id(aln))),
                   as.character(id(aln0)))
    colidx <- varLabels(alignData(aln)) != "pairedReadNumber"
    checkIdentical(alignData(aln)[, colidx], alignData(aln0))
}

test_AlignedRead_readAligned_MAQMapview <- function() {
    fl <- system.file("extdata", "maq", package="ShortRead")
    obj <- readAligned(fl, pattern=".*aln.*", type="MAQMapview")
    checkTrue(validObject(obj))
    checkTrue(is(quality(obj), "FastqQuality"))
    checkTrue(is(alignQuality(obj), "NumericQuality"))
    checkIdentical(varLabels(alignData(obj)),
                   c("nMismatchBestHit", "mismatchQuality",
                   "nExactMatch24", "nOneMismatch24"))
    checkIdentical(levels(chromosome(obj)), "ChrA")
    checkTrue(!any(is.na(chromosome(obj))) &&
              !any(is.null(chromosome(obj))))
}

readAligned_maq_consistent <- function() {
    ## FIXME: find adequate data to store in ShortRead pkg
    if (!file.exists("/home/jdavison/sharedrsrc/proj/ycao/data/binary_maps/s_5.map"))
        return(TRUE)

    x <- readAligned("/home/jdavison/sharedrsrc/proj/ycao/data/binary_maps",
                     "s_5.map", "MAQMap")
    y <- readAligned("/home/jdavison/sharedrsrc/proj/ycao/data/text_maps",
                     "s_5.txt", "MAQMapview")

    checkIdentical(length(x), length(y))
    checkIdentical(width(x), width(y))
    checkIdentical(as.character(chromosome(x)), as.character(chromosome(y)))

    ## FIXME: we'd really like chromosome to have identical levels,
    ## but info on levels with no mapped reads is not available in the
    ## text version
    idx <- match(levels(chromosome(y)), levels(chromosome(x)))
    checkTrue(all(!is.na(idx)) && all(diff(idx) > 0))
    checkIdentical(position(x), position(y))
    checkIdentical(strand(x), strand(y))
    checkIdentical(alignQuality(x), alignQuality(y))
    checkIdentical(alignData(x), alignData(y))

    .checkXString <- function(x, y) {
        checkIdentical(as.character(x), as.character(y))
    }
    .checkXString(sread(x), sread(y))
    .checkXString(sread(x), sread(y))
    .checkXString(quality(quality(x)), quality(quality(y)))
    .checkXString(id(x), id(y))
}

test_AlignedRead_readAligned_run_as_factor <- function()
{
    src <- system.file("unitTests", "cases", package="ShortRead")
    aln <- readAligned(src, "^s_2_export_run_as_factor.txt$",
                       "SolexaExport")
    checkIdentical(alignData(aln)[["run"]],
                   factor(rep("genome", length(aln))))
}

test_AlignedRead_readAligned_realign_targetpos <- function()
{
    ## column 4 can be target:pos
    fl <- "s_2_0001_realign_head.txt"
    src <- system.file("unitTests", "cases", package="ShortRead")
    tbl <- read.table(file.path(src, fl), fill=TRUE)
    aln <- readAligned(src, fl, "SolexaRealign")
    checkIdentical(as.character(tbl[[1]]), as.character(sread(aln)))
    checkIdentical(tbl[[2]], quality(alignQuality(aln)))
    checkIdentical(tbl[[3]], alignData(aln)[["nMatch"]])
    checkIdentical(table(tbl[[5]])[["F"]], table(strand(aln))[["+"]])
    chr <- sub(":.*", "", tbl[[4]])
    chr[nchar(chr)==0] <- NA
    checkIdentical(factor(chr), chromosome(aln))
    checkIdentical(as.integer(sub(".*:", "", tbl[[4]])), position(aln))
    checkIdentical(ShortRead:::.toStrand_Solexa(tbl[[5]]), strand(aln))
    checkIdentical(tbl[[7]], alignData(aln)[["nextBestAlignQuality"]])
}

test_AlignedRead_readAligned_realign_threecol <- function()
{
    ## column 4 can be target:pos
    fl <- "s_2_0001_realign_3col_head.txt"
    src <- system.file("unitTests", "cases", package="ShortRead")
    tbl <- read.table(file.path(src, fl), fill=TRUE)
    aln <- readAligned(src, fl, "SolexaRealign")
    checkIdentical(as.character(tbl[[1]]), as.character(sread(aln)))
    checkIdentical(tbl[[2]], quality(alignQuality(aln)))
    checkIdentical(tbl[[3]], alignData(aln)[["nMatch"]])
    checkIdentical(factor(rep(NA_character_, nrow(tbl))), chromosome(aln))
    checkIdentical(rep(NA_integer_, nrow(tbl)), position(aln))
    checkIdentical(ShortRead:::.toStrand_Solexa(rep("", nrow(tbl))),
                   strand(aln))
    checkIdentical(rep(NA_integer_, nrow(tbl)),
                   alignData(aln)[["nextBestAlignQuality"]])
}

test_AlignedRead_readAligned_SolexaResult <- function()
{
    fl <- "s_1_results_head.txt"
    src <- system.file("unitTests", "cases", package="ShortRead")
    tbl <- read.table(file.path(src, fl), fill=TRUE,
                      col.names=paste("V", 1:12, sep=""),
                      stringsAsFactors = TRUE)
    aln <- readAligned(src, fl, "SolexaResult")
    
    checkIdentical(as.character(tbl[[2]]), as.character(sread(aln)))
    chr <- tbl[[7]]
    checkIdentical(factor(chr), chromosome(aln))
    checkIdentical(tbl[[8]], position(aln))
    checkIdentical(ShortRead:::.toStrand_Solexa(tbl[[9]]), strand(aln))

    ad <- alignData(aln)
    checkIdentical(tbl[[3]], ad[[1]])
    checkIdentical(tbl[[4]], ad[[2]])
    checkIdentical(tbl[[5]], ad[[3]])
    checkIdentical(tbl[[6]], ad[[4]])

    checkIdentical(tbl[[10]], ad[[5]])
    checkIdentical(as.character(tbl[[11]]), ad[[6]])
    checkIdentical(as.character(tbl[[12]]), ad[[7]])
}

test_AlignedRead_constructor <- function()
{
    aln <- AlignedRead()
    checkTrue(validObject(aln))

    aln <- AlignedRead(sread=DNAStringSet(polyn("A", 5)))
    checkTrue(validObject(aln))

    aln <- AlignedRead(sread=DNAStringSet(
                         c(polyn("A", 5), polyn("A", 10))))
    checkTrue(validObject(aln))
    checkIdentical(c(5L, 10L), width(aln))
}

test_AlignedRead_compact <- function() {
    exp <- aln[1:100]
    obs <- compact(exp)
    checkIdentical(as.character(sread(exp)), as.character(sread(obs)))
    checkIdentical(as.character(quality(quality(exp))),
                   as.character(quality(quality(obs))))
    checkIdentical(as.character(id(exp)), as.character(id(obs)))
    checkIdentical(alignData(exp), alignData(obs))
}