tests/testthat/test_src.R
In fmicompbio/QuasR: Quantify and Annotate Short Reads in R
# cover parts that are not already covered indirectly by other tests
context("compiled code")
test_that("extractUnmappedReads works as expected", {
fun <- function(...) .Call(QuasR:::extractUnmappedReads, ...)
bamf1 <- pChipSingle@alignments$FileName[1]
bamf2 <- pRnaPaired@alignments$FileName[1]
fafile <- tempfile(fileext = rep(".fa",2), tmpdir = "extdata")
fqfile <- tempfile(fileext = rep(".fq",2), tmpdir = "extdata")
# arguments
expect_error(fun(1L, fafile[1], FALSE, FALSE))
expect_error(fun(bamf1, 1L, FALSE, FALSE))
expect_error(fun(bamf1, fafile[1], 1L, FALSE))
expect_error(fun(bamf1, fafile[1], FALSE, 1L))
expect_error(fun("no-file", fafile[1], FALSE, FALSE))
expect_error(fun(genomeFile, fafile[1], FALSE, FALSE))
expect_error(fun(bamf1, "not-there/fafile", FALSE, FALSE))
# results
f <- fun(bamf1, fafile[1], FALSE, FALSE); expect_length(readLines(f), 516L)
f <- fun(bamf1, fafile[1], FALSE, TRUE); expect_length(readLines(f), 516L)
f <- fun(bamf1, fqfile[1], TRUE, FALSE); expect_length(readLines(f), 1032L)
f <- fun(bamf1, fqfile[1], TRUE, TRUE); expect_length(readLines(f), 1032L)
f <- fun(bamf2, fafile, FALSE, FALSE); expect_length(readLines(f[1]), 3746L)
f <- fun(bamf2, fafile, FALSE, TRUE); expect_length(readLines(f[2]), 3746L)
f <- fun(bamf2, fqfile, TRUE, FALSE); expect_length(readLines(f[1]), 7492L)
f <- fun(bamf2, fqfile, TRUE, TRUE); expect_length(readLines(f[2]), 7492L)
})
test_that("catBam works as expected", {
requireNamespace("Rsamtools")
fun <- function(...) .Call(QuasR:::catBam, ...)
bamf1 <- pSingle@alignments$FileName[1]
bfile <- tempfile(fileext = ".bam", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, bfile))
expect_error(fun(bamf1, 1L))
expect_error(fun(bamf1, "not-there/bfile"))
# results
expect_identical(fun(bamf1, bfile), 0L)
Rsamtools::indexBam(bfile)
expect_identical(alignmentStats(bamf1)[1,],
alignmentStats(bfile)[1,])
})
test_that("splitSamChr works as expected", {
fun <- function(...) .Call(QuasR:::splitSamChr, ...)
bamf1 <- pSingle@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
outdir <- tempfile(pattern = "sam", tmpdir = "extdata")
dir.create(outdir)
# arguments
expect_error(fun( 1L, outdir))
expect_error(fun(samf1, 1L))
# results
chrs <- fun(samf1, outdir)
expect_identical(chrs, c("chrV", "splitChrSam_unaligned"))
expect_identical(list.files(outdir), paste0(chrs, ".sam"))
expect_length(readLines(file.path(outdir, "chrV.sam")), 514L)
expect_length(readLines(file.path(outdir, "splitChrSam_unaligned.sam")), 2L)
unlink(outdir, recursive = TRUE, force = TRUE)
})
test_that("countJunctions works as expected", {
fun <- function(...) .Call(QuasR:::countJunctions, ...)
bamf1 <- pSingleAllelic@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
# arguments
expect_error(fun( 1L, 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, "", 0L, 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, "", 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, "", FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, "", FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, "", 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, -1, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, 0L, -1))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, 2L, 1L))
expect_error(fun("err", 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(samf1, 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L))
# results
r1 <- fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L)
r2 <- fun(bamf1, 0L, 0L, 1000L, TRUE, FALSE, 0L, 255L)
expect_is(r1, "integer")
expect_length(r1, 512L)
expect_is(r2, "list")
expect_length(r2, 4L)
expect_true(all(lengths(r2) == 512L))
})
test_that("bamfileToWig works as expected", {
fun <- function(...) .Call(QuasR:::bamfileToWig, ...)
bamf1 <- pSingle@alignments$FileName[1]
wig1 <- tempfile(fileext = ".wig", tmpdir = "extdata")
wig2 <- tempfile(fileext = ".wig.gz", tmpdir = "extdata")
wig3 <- tempfile(fileext = ".wig", tmpdir = "extdata")
wig4 <- tempfile(fileext = ".wig.gz", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, 1L, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, "", 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, "", 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, "", "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, 1L, 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", "", "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, 1L, FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", 1L,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
1L, FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", 1L, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, 1L, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, "", 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, "", 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, "", 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, "", 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, ""))
expect_error(fun("err", wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
# results
r1 <- fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 800L, 16L)
r2 <- fun(bamf1, wig3, FALSE, 20L, 0L, "*", 1.0, "trackname", TRUE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 800L, 16L)
r3 <- fun(bamf1, wig2, FALSE, 15L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", TRUE, FALSE, 0L, 255L, 0L, 800L, 16L)
r4 <- fun(bamf1, wig4, FALSE, 30L, 0L, "*", 1.0, "trackname", TRUE,
"255,212,0", TRUE, FALSE, 0L, 255L, 0L, 800L, 16L)
l1 <- readLines(wig1)
l2 <- readLines(wig2)
l3 <- readLines(wig3)
l4 <- readLines(wig4)
expect_length(l1, 82L)
expect_length(l2, 55L)
expect_length(l3, 42L)
expect_length(l4, 28L)
expect_identical(sum(as.numeric(l1[-c(1, 2)])), sum(as.numeric(l2[-c(1, 2)])))
expect_equal(sum(as.numeric(l3[-c(1, 2)])), 113.45)
expect_equal(sum(as.numeric(l4[-c(1, 2)])), 85.73)
})
test_that("mergeReorderSam works as expected", {
fun <- function(...) .Call(QuasR:::mergeReorderSam, ...)
bamf1 <- pPaired@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
samf2 <- tempfile(fileext = ".sam", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, samf2, 0L, 1L))
expect_error(fun(samf1, 1L, 0L, 1L))
expect_error(fun(samf1, samf2, "", 1L))
expect_error(fun(samf1, samf2, 0L, ""))
expect_error(fun(samf1, samf2, 4L, 1L))
expect_error(fun(samf1, samf2, 1L, 1L))
expect_error(fun(samf1, samf2, 2L, 1L))
expect_error(fun(samf1, "err/err", 0L, 1L))
# results
expect_identical(fun(rep(samf1, 2), samf2, 0L, 1L), 1L)
expect_length(readLines(samf2), 44L)
expect_identical(fun(rep(samf1, 2), samf2, 2L, 1L), 1L)
expect_length(readLines(samf2), 24L)
})
test_that("removeUnmappedFromSamAndConvertToBam works as expected", {
fun <- function(...) .Call(QuasR:::removeUnmappedFromSamAndConvertToBam, ...)
bamf1 <- pPaired@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
bamf2 <- tempfile(fileext = ".bam", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, bamf2))
expect_error(fun(samf1, 1L))
expect_error(fun("err", bamf2))
expect_error(fun(samf1, "err/err"))
# results
expect_identical(fun(samf1, bamf2), bamf2)
})
test_that("filterHisat2 works as expected", {
# create example sam file
fun <- function(...) .Call(QuasR:::filterHisat2, ...)
samf1 <- tempfile(fileext = ".sam", tmpdir = "extdata")
samf2 <- tempfile(fileext = ".sam", tmpdir = "extdata")
writeLines(text = c("@HD\tVN:1.4",
"@SQ\tSN:chr1\tLN:40000",
"@SQ\tSN:chr2\tLN:10000",
"@SQ\tSN:chr3\tLN:45000",
"seq1\t163\tchr3\t12355\t255\t38M560N12M\t=\t13074\t769\tCAGCCCTTGAACGGAGAATAGAGTACATTGAAGCTCGGGTGACAAAAGGT\tggggggggggggggggggggggggggggghggggfggegccceacLSSTS\tNH:i:1",
"seq1\t83\tchr3\t13074\t255\t50M\t=\t12355\t-769\tAGAGCAACAGGGCTTATTCTTGTTTTTCTTTTTTCAAAAGTGTGGCCTTT\tgggggggggggggggggggggggfffffffffgggggggggggggggggg\tNH:i:1",
"seq2\t163\tchr2\t2927\t255\t14M241N36M\t=\t3424\t547\tCGGCGCTCGGCAAGTTCTCCCAGGAGAAAGCCATGTTCAGTTCGAGCGCC\tgggggggggghgggfggggggdggggggggggggggggggefeggdgggg\tNH:i:2",
"seq2\t83\tchr2\t3424\t255\t50M\t=\t2927\t-547\tGATGAACTCGGACCTCAAGGCTCAGCTCAGGGAGCTGAATATTACGGCAG\tgggggggggggggfggggggggggggfgggfggggggggggggggggghg\tNH:i:2",
"seq3\t163\tchr2\t5346\t255\t19M2335N31M\t=\t7796\t2500\tAGCAAAAGCGTCCCAGGAGCCGTACTCTGACAGCTGTGCACGATGCCATC\tgggggggggggggggggfggggggggggggggggdggggggggggegggg\tNH:i:3",
"seq3\t83\tchr2\t7796\t255\t50M\t=\t5346\t-2500\tCCGGCTCATAAAGGTTCATTTGGACAAAGCACAGCAGAACAATGTGGAAC\tgggggggggggggggggggggggggggggggggggggggggggggggggg\tNH:i:3",
"seq4\t99\tchr3\t2413\t255\t50M\t=\t12343\t9980\tCGGGAGATTCACCAGGACTGGGCTGACCAGGAGTACATTGAGATAATCAC\teggegddceedggggeZcec^]`^`ffffcTTSUTTSSTTfffaf]``]^\tNH:i:4",
"seq4\t147\tchr3\t12343\t255\t50M\t=\t2413\t-9980\tACGAGAAATTGACAGCCCTTGAACGGAGAATAGAGTACATTGAAGCTCGG\tacaaccaeccTTTSS_]_]`__P__SSTTTgdgggghgbgTTTTSggggg\tNH:i:4",
"seq5\t419\tchr1\t23628\t255\t50M\t=\t24226\t648\tCTCGTCCACTTTGAGTTCCTCGTTGAGCCTGATGGCGTCGGCAACCTCCT\tggfegfeeffTSSTSd`bbcc^c```^cc[aeefa_TT[ZTTTTTZ_[ZZ\tNH:i:1",
"seq5\t339\tchr1\t24226\t255\t50M\t=\t23628\t-648\tTCCACGGCGCGGAAGTGTGTCTTGCTCTCCTCCATGGCCTCCTGGAAGTG\tgggggggfgfW`]``ggggggfdgd^^c``[d_cbgdggggdgeggggb^\tNH:i:1",
"seq6\t77\t*\t0\t0\t*\t*\t0\t0\tGCCGCCCTCGCAGTGCTGCCAGAGAAGGGAGGGCATCCCCTGAGCCGCCG\tggggggggggggggggggggggggggggggggfffggggggggggdgggg",
"seq6\t141\t*\t0\t0\t*\t*\t0\t0\tGGCCCCAAGGCCCCCGTCCCGCAGCCACGCTTGTGGTCGCTGCGTCCCGG\tgggggggggggggggggggggggggggdgcgggedbe`^bEbV__ed^bc"),
con = samf1)
# arguments
expect_error(fun( 1L, samf2, 1L))
expect_error(fun(samf1, 1L, 1L))
expect_error(fun(samf1, samf2, "1L"))
expect_error(fun("err", samf2, 1L))
# results
r0 <- fun(samf1, samf2, 0L); n0 <- length(readLines(samf2))
r1 <- fun(samf1, samf2, 1L); n1 <- length(readLines(samf2))
r2 <- fun(samf1, samf2, 2L); n2 <- length(readLines(samf2))
r3 <- fun(samf1, samf2, 3L); n3 <- length(readLines(samf2))
r4 <- fun(samf1, samf2, 4L); n4 <- length(readLines(samf2))
expect_identical(n0, 14L)
expect_identical(n1, 14L)
expect_identical(n2, 14L)
expect_identical(n3, 14L)
expect_identical(n4, 14L)
expect_identical(r0, c(n_secondary=2L, n_overmapped=8L))
expect_identical(r1, c(n_secondary=2L, n_overmapped=6L))
expect_identical(r2, c(n_secondary=2L, n_overmapped=4L))
expect_identical(r3, c(n_secondary=2L, n_overmapped=2L))
expect_identical(r4, c(n_secondary=2L, n_overmapped=0L))
})
fmicompbio/QuasR documentation built on Nov. 1, 2024, 9:08 p.m.
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# cover parts that are not already covered indirectly by other tests
context("compiled code")
test_that("extractUnmappedReads works as expected", {
fun <- function(...) .Call(QuasR:::extractUnmappedReads, ...)
bamf1 <- pChipSingle@alignments$FileName[1]
bamf2 <- pRnaPaired@alignments$FileName[1]
fafile <- tempfile(fileext = rep(".fa",2), tmpdir = "extdata")
fqfile <- tempfile(fileext = rep(".fq",2), tmpdir = "extdata")
# arguments
expect_error(fun(1L, fafile[1], FALSE, FALSE))
expect_error(fun(bamf1, 1L, FALSE, FALSE))
expect_error(fun(bamf1, fafile[1], 1L, FALSE))
expect_error(fun(bamf1, fafile[1], FALSE, 1L))
expect_error(fun("no-file", fafile[1], FALSE, FALSE))
expect_error(fun(genomeFile, fafile[1], FALSE, FALSE))
expect_error(fun(bamf1, "not-there/fafile", FALSE, FALSE))
# results
f <- fun(bamf1, fafile[1], FALSE, FALSE); expect_length(readLines(f), 516L)
f <- fun(bamf1, fafile[1], FALSE, TRUE); expect_length(readLines(f), 516L)
f <- fun(bamf1, fqfile[1], TRUE, FALSE); expect_length(readLines(f), 1032L)
f <- fun(bamf1, fqfile[1], TRUE, TRUE); expect_length(readLines(f), 1032L)
f <- fun(bamf2, fafile, FALSE, FALSE); expect_length(readLines(f[1]), 3746L)
f <- fun(bamf2, fafile, FALSE, TRUE); expect_length(readLines(f[2]), 3746L)
f <- fun(bamf2, fqfile, TRUE, FALSE); expect_length(readLines(f[1]), 7492L)
f <- fun(bamf2, fqfile, TRUE, TRUE); expect_length(readLines(f[2]), 7492L)
})
test_that("catBam works as expected", {
requireNamespace("Rsamtools")
fun <- function(...) .Call(QuasR:::catBam, ...)
bamf1 <- pSingle@alignments$FileName[1]
bfile <- tempfile(fileext = ".bam", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, bfile))
expect_error(fun(bamf1, 1L))
expect_error(fun(bamf1, "not-there/bfile"))
# results
expect_identical(fun(bamf1, bfile), 0L)
Rsamtools::indexBam(bfile)
expect_identical(alignmentStats(bamf1)[1,],
alignmentStats(bfile)[1,])
})
test_that("splitSamChr works as expected", {
fun <- function(...) .Call(QuasR:::splitSamChr, ...)
bamf1 <- pSingle@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
outdir <- tempfile(pattern = "sam", tmpdir = "extdata")
dir.create(outdir)
# arguments
expect_error(fun( 1L, outdir))
expect_error(fun(samf1, 1L))
# results
chrs <- fun(samf1, outdir)
expect_identical(chrs, c("chrV", "splitChrSam_unaligned"))
expect_identical(list.files(outdir), paste0(chrs, ".sam"))
expect_length(readLines(file.path(outdir, "chrV.sam")), 514L)
expect_length(readLines(file.path(outdir, "splitChrSam_unaligned.sam")), 2L)
unlink(outdir, recursive = TRUE, force = TRUE)
})
test_that("countJunctions works as expected", {
fun <- function(...) .Call(QuasR:::countJunctions, ...)
bamf1 <- pSingleAllelic@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
# arguments
expect_error(fun( 1L, 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, "", 0L, 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, "", 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, "", FALSE, FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, "", FALSE, 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, "", 0L, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, -1, 255L))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, 0L, -1))
expect_error(fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, 2L, 1L))
expect_error(fun("err", 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L))
expect_error(fun(samf1, 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L))
# results
r1 <- fun(bamf1, 0L, 0L, 1000L, FALSE, FALSE, 0L, 255L)
r2 <- fun(bamf1, 0L, 0L, 1000L, TRUE, FALSE, 0L, 255L)
expect_is(r1, "integer")
expect_length(r1, 512L)
expect_is(r2, "list")
expect_length(r2, 4L)
expect_true(all(lengths(r2) == 512L))
})
test_that("bamfileToWig works as expected", {
fun <- function(...) .Call(QuasR:::bamfileToWig, ...)
bamf1 <- pSingle@alignments$FileName[1]
wig1 <- tempfile(fileext = ".wig", tmpdir = "extdata")
wig2 <- tempfile(fileext = ".wig.gz", tmpdir = "extdata")
wig3 <- tempfile(fileext = ".wig", tmpdir = "extdata")
wig4 <- tempfile(fileext = ".wig.gz", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, 1L, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, "", 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, "", 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, "", "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, 1L, 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", "", "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, 1L, FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", 1L,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
1L, FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", 1L, FALSE, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, 1L, 0L, 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, "", 255L, 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, "", 0L, 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, "", 1000L, 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, "", 16L))
expect_error(fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, ""))
expect_error(fun("err", wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 1000L, 16L))
# results
r1 <- fun(bamf1, wig1, FALSE, 10L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 800L, 16L)
r2 <- fun(bamf1, wig3, FALSE, 20L, 0L, "*", 1.0, "trackname", TRUE,
"255,212,0", FALSE, FALSE, 0L, 255L, 0L, 800L, 16L)
r3 <- fun(bamf1, wig2, FALSE, 15L, 0L, "*", 1.0, "trackname", FALSE,
"255,212,0", TRUE, FALSE, 0L, 255L, 0L, 800L, 16L)
r4 <- fun(bamf1, wig4, FALSE, 30L, 0L, "*", 1.0, "trackname", TRUE,
"255,212,0", TRUE, FALSE, 0L, 255L, 0L, 800L, 16L)
l1 <- readLines(wig1)
l2 <- readLines(wig2)
l3 <- readLines(wig3)
l4 <- readLines(wig4)
expect_length(l1, 82L)
expect_length(l2, 55L)
expect_length(l3, 42L)
expect_length(l4, 28L)
expect_identical(sum(as.numeric(l1[-c(1, 2)])), sum(as.numeric(l2[-c(1, 2)])))
expect_equal(sum(as.numeric(l3[-c(1, 2)])), 113.45)
expect_equal(sum(as.numeric(l4[-c(1, 2)])), 85.73)
})
test_that("mergeReorderSam works as expected", {
fun <- function(...) .Call(QuasR:::mergeReorderSam, ...)
bamf1 <- pPaired@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
samf2 <- tempfile(fileext = ".sam", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, samf2, 0L, 1L))
expect_error(fun(samf1, 1L, 0L, 1L))
expect_error(fun(samf1, samf2, "", 1L))
expect_error(fun(samf1, samf2, 0L, ""))
expect_error(fun(samf1, samf2, 4L, 1L))
expect_error(fun(samf1, samf2, 1L, 1L))
expect_error(fun(samf1, samf2, 2L, 1L))
expect_error(fun(samf1, "err/err", 0L, 1L))
# results
expect_identical(fun(rep(samf1, 2), samf2, 0L, 1L), 1L)
expect_length(readLines(samf2), 44L)
expect_identical(fun(rep(samf1, 2), samf2, 2L, 1L), 1L)
expect_length(readLines(samf2), 24L)
})
test_that("removeUnmappedFromSamAndConvertToBam works as expected", {
fun <- function(...) .Call(QuasR:::removeUnmappedFromSamAndConvertToBam, ...)
bamf1 <- pPaired@alignments$FileName[1]
samf1 <- sub(".bam$", ".sam", bamf1)
bamf2 <- tempfile(fileext = ".bam", tmpdir = "extdata")
# arguments
expect_error(fun( 1L, bamf2))
expect_error(fun(samf1, 1L))
expect_error(fun("err", bamf2))
expect_error(fun(samf1, "err/err"))
# results
expect_identical(fun(samf1, bamf2), bamf2)
})
test_that("filterHisat2 works as expected", {
# create example sam file
fun <- function(...) .Call(QuasR:::filterHisat2, ...)
samf1 <- tempfile(fileext = ".sam", tmpdir = "extdata")
samf2 <- tempfile(fileext = ".sam", tmpdir = "extdata")
writeLines(text = c("@HD\tVN:1.4",
"@SQ\tSN:chr1\tLN:40000",
"@SQ\tSN:chr2\tLN:10000",
"@SQ\tSN:chr3\tLN:45000",
"seq1\t163\tchr3\t12355\t255\t38M560N12M\t=\t13074\t769\tCAGCCCTTGAACGGAGAATAGAGTACATTGAAGCTCGGGTGACAAAAGGT\tggggggggggggggggggggggggggggghggggfggegccceacLSSTS\tNH:i:1",
"seq1\t83\tchr3\t13074\t255\t50M\t=\t12355\t-769\tAGAGCAACAGGGCTTATTCTTGTTTTTCTTTTTTCAAAAGTGTGGCCTTT\tgggggggggggggggggggggggfffffffffgggggggggggggggggg\tNH:i:1",
"seq2\t163\tchr2\t2927\t255\t14M241N36M\t=\t3424\t547\tCGGCGCTCGGCAAGTTCTCCCAGGAGAAAGCCATGTTCAGTTCGAGCGCC\tgggggggggghgggfggggggdggggggggggggggggggefeggdgggg\tNH:i:2",
"seq2\t83\tchr2\t3424\t255\t50M\t=\t2927\t-547\tGATGAACTCGGACCTCAAGGCTCAGCTCAGGGAGCTGAATATTACGGCAG\tgggggggggggggfggggggggggggfgggfggggggggggggggggghg\tNH:i:2",
"seq3\t163\tchr2\t5346\t255\t19M2335N31M\t=\t7796\t2500\tAGCAAAAGCGTCCCAGGAGCCGTACTCTGACAGCTGTGCACGATGCCATC\tgggggggggggggggggfggggggggggggggggdggggggggggegggg\tNH:i:3",
"seq3\t83\tchr2\t7796\t255\t50M\t=\t5346\t-2500\tCCGGCTCATAAAGGTTCATTTGGACAAAGCACAGCAGAACAATGTGGAAC\tgggggggggggggggggggggggggggggggggggggggggggggggggg\tNH:i:3",
"seq4\t99\tchr3\t2413\t255\t50M\t=\t12343\t9980\tCGGGAGATTCACCAGGACTGGGCTGACCAGGAGTACATTGAGATAATCAC\teggegddceedggggeZcec^]`^`ffffcTTSUTTSSTTfffaf]``]^\tNH:i:4",
"seq4\t147\tchr3\t12343\t255\t50M\t=\t2413\t-9980\tACGAGAAATTGACAGCCCTTGAACGGAGAATAGAGTACATTGAAGCTCGG\tacaaccaeccTTTSS_]_]`__P__SSTTTgdgggghgbgTTTTSggggg\tNH:i:4",
"seq5\t419\tchr1\t23628\t255\t50M\t=\t24226\t648\tCTCGTCCACTTTGAGTTCCTCGTTGAGCCTGATGGCGTCGGCAACCTCCT\tggfegfeeffTSSTSd`bbcc^c```^cc[aeefa_TT[ZTTTTTZ_[ZZ\tNH:i:1",
"seq5\t339\tchr1\t24226\t255\t50M\t=\t23628\t-648\tTCCACGGCGCGGAAGTGTGTCTTGCTCTCCTCCATGGCCTCCTGGAAGTG\tgggggggfgfW`]``ggggggfdgd^^c``[d_cbgdggggdgeggggb^\tNH:i:1",
"seq6\t77\t*\t0\t0\t*\t*\t0\t0\tGCCGCCCTCGCAGTGCTGCCAGAGAAGGGAGGGCATCCCCTGAGCCGCCG\tggggggggggggggggggggggggggggggggfffggggggggggdgggg",
"seq6\t141\t*\t0\t0\t*\t*\t0\t0\tGGCCCCAAGGCCCCCGTCCCGCAGCCACGCTTGTGGTCGCTGCGTCCCGG\tgggggggggggggggggggggggggggdgcgggedbe`^bEbV__ed^bc"),
con = samf1)
# arguments
expect_error(fun( 1L, samf2, 1L))
expect_error(fun(samf1, 1L, 1L))
expect_error(fun(samf1, samf2, "1L"))
expect_error(fun("err", samf2, 1L))
# results
r0 <- fun(samf1, samf2, 0L); n0 <- length(readLines(samf2))
r1 <- fun(samf1, samf2, 1L); n1 <- length(readLines(samf2))
r2 <- fun(samf1, samf2, 2L); n2 <- length(readLines(samf2))
r3 <- fun(samf1, samf2, 3L); n3 <- length(readLines(samf2))
r4 <- fun(samf1, samf2, 4L); n4 <- length(readLines(samf2))
expect_identical(n0, 14L)
expect_identical(n1, 14L)
expect_identical(n2, 14L)
expect_identical(n3, 14L)
expect_identical(n4, 14L)
expect_identical(r0, c(n_secondary=2L, n_overmapped=8L))
expect_identical(r1, c(n_secondary=2L, n_overmapped=6L))
expect_identical(r2, c(n_secondary=2L, n_overmapped=4L))
expect_identical(r3, c(n_secondary=2L, n_overmapped=2L))
expect_identical(r4, c(n_secondary=2L, n_overmapped=0L))
})
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