tests/testthat/test_digestFastqs_helpers.R
In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data
## ----------------------------------------------------------------------------
## compareCodonPositions
## ----------------------------------------------------------------------------
test_that("compareCodonPositions works", {
expect_true(compareCodonPositions("f.1.AAA_", "f.2.ACT_", "."))
expect_true(compareCodonPositions("f.2.ACT_", "f.10.TCA_", "."))
})
## ----------------------------------------------------------------------------
## findClosestRefSeq
## ----------------------------------------------------------------------------
test_that("findClosestRefSeq works", {
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ACGT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 0L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ACG", "ACGT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("AACGT", "ACCTA"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 0L, sim = 0L), -1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ATGT", "ACTT"),
upperBoundMismatch = 1L, sim = 0L), -2L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ACGT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 0L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ACG", "ACGT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("AACGT", "ACCTA"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 0L, sim = 0L), -1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ATGT", "ACTT"),
upperBoundMismatch = 1L, sim = 0L), -2L)
})
## ----------------------------------------------------------------------------
## decomposeRead
## ----------------------------------------------------------------------------
test_that("decomposeRead works", {
## All element lengths specified, no primer
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVCUSV",
elementLengths = c(2, 1, 3, 3, 1, 2, 1, 1), primerSeqs = "",
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "", nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACCT")
expect_equal(res$varSeq, "AAGG")
expect_equal(res$varQual, "gABG")
expect_equal(res$varLengths, c(3L, 1L))
expect_equal(res$constSeq, "TTAC")
expect_equal(res$constQual, "defC")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## All element lengths specified, no primer, 0 lengths included
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTG", squal = "abcdefgABCDEF", elements = "SUSCVUCUS",
elementLengths = c(0, 2, 1, 3, 3, 0, 1, 2, 1), primerSeqs = "",
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACCT")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTAC")
expect_equal(res$constQual, "defC")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Derive variable length from other lengths
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTG", squal = "abcdefgABCDEF", elements = "USCVCUS",
elementLengths = c(2, 1, 3, -1, 1, 2, 1), primerSeqs = "",
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACCT")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTAC")
expect_equal(res$constQual, "defC")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVPS",
elementLengths = c(2, 1, 3, 3, 3, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Only variable sequence
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "V",
elementLengths = -1, primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "ACGTTAAAGCCTGG")
expect_equal(res$varQual, "abcdefgABCDEFG")
expect_equal(res$varLengths, 14L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer + variable sequence
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "PV",
elementLengths = c(-1, -1), primerSeqs = c("ACG"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "TTAAAGCCTGG")
expect_equal(res$varQual, "defgABCDEFG")
expect_equal(res$varLengths, 11L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Variable sequence + primer
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VP",
elementLengths = c(-1, -1), primerSeqs = c("ACG"),
varSeq = "A", varQual = "E", varLengths = 1L, umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "A")
expect_equal(res$varQual, "E")
expect_equal(res$varLengths, c(1L, 0L))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer, not the right length of sequence
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VPU",
elementLengths = c(10, 3, 2), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 1)
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VPU",
elementLengths = c(8, 3, 2), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 1)
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "CVPU",
elementLengths = c(10, -1, 3, 2), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 1)
## Primer, but don't explicitly specify that the part after the primer should be skipped
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Multiple primers, only one present
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("TTT", "CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Multiple primers, none present
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("TTT", "GGG"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 1)
expect_equal(res$nReadWrongLength, 0)
## Multiple primers, all present (use the first one)
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("CCT", "TTA"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer, infer length of sequences
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "UPV",
elementLengths = c(-1, 3, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACGTTAAAG")
expect_equal(res$varSeq, "GG")
expect_equal(res$varQual, "FG")
expect_equal(res$varLengths, 2L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer, don't specify primer length
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "UPV",
elementLengths = c(-1, -1, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACGTTAAAG")
expect_equal(res$varSeq, "GG")
expect_equal(res$varQual, "FG")
expect_equal(res$varLengths, 2L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Multiple variable segments with different lengths
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VPV",
elementLengths = c(-1, -1, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "ACGTTAAAGGG")
expect_equal(res$varQual, "abcdefgABFG")
expect_equal(res$varLengths, c(9L, 2L))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
})
## ----------------------------------------------------------------------------
## mergeReadPairsPartial
## ----------------------------------------------------------------------------
test_that("mergeReadPairsPartial works", {
## don't count N as mismatch, pick base with higher quality
sF1 <- "AAAANA"; qF1 <- rep(40L, nchar(sF1)); lF1 <- 6L
sR1 <- "AACCCC"; qR1 <- rep(42L, nchar(sR1)); lR1 <- 6L
res1a <- mutscan:::test_mergeReadPairPartial(sF1, qF1, sR1, qR1, lF1, lR1, 1, 6, 0, 0, 1/4, TRUE)
res1b <- mutscan:::test_mergeReadPairPartial(sF1, qF1, sR1, qR1, lF1, lR1, 1, 6, 0, 0, 1/4, FALSE)
res1c <- mutscan:::test_mergeReadPairPartial(sF1, qR1, sR1, qF1, lF1, lR1, 2, 2, 0, 0, 1/4, TRUE)
res1d <- mutscan:::test_mergeReadPairPartial(sF1, qF1, sR1, qR1, lF1, lR1, 2, 2, 0, 0, 0, TRUE)
expect_type(res1a, "list")
expect_type(res1b, "list")
expect_type(res1c, "list")
expect_type(res1d, "list")
expect_identical(res1a$mergedSeq, "AAAACCCC")
expect_identical(res1a$mergedQual, rep(c(40L, 42L), c(2, 6)))
expect_identical(res1a$mergedLengths, 8L)
expect_identical(res1a, res1b)
expect_identical(res1c$mergedSeq, "AAAANACCCC")
expect_identical(res1d$mergedSeq, "AAAAAACCCC")
expect_identical(res1c$mergedLengths, 10L)
expect_identical(res1d$mergedLengths, 10L)
## no valid overlap, multiple possible overlaps with single mismatch
sF2 <- "TTACACG"; qF2 <- rep(10L, nchar(sF2)); lF2 <- 7L
sR2 <- "ACACACA"; qR2 <- rep(40L, nchar(sR2)); lR2 <- 7L
res2a <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 0, 0, 0, 0, maxFracMismatchOverlap = 3/7, TRUE)
res2b <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 0, 0, 1/5, TRUE)
expect_type(res2a, "list")
expect_type(res2b, "list")
expect_identical(res2a$mergedSeq, sR2)
expect_identical(res2a$mergedQual, qR2)
expect_identical(res2a$mergedLengths, 7L)
expect_identical(res2b$mergedSeq, "TTACACACA")
expect_identical(res2b$mergedQual, rep(c(10L,40L), c(2,7)))
expect_identical(res2b$mergedLengths, 9L)
## specify min/max merged length instead
res2c <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 9, 9, 1, FALSE)
res2d <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 11, 11, 1, FALSE)
res2e <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 12, 12, 1, FALSE)
expect_type(res2c, "list")
expect_type(res2d, "list")
expect_type(res2e, "list")
expect_identical(res2c$mergedSeq, "TTACACACA")
expect_identical(res2c$mergedQual, rep(c(10L, 40L), c(2, 7)))
expect_identical(res2c$mergedLengths, 9L)
expect_identical(res2d$mergedSeq, "TTACACACACA")
expect_identical(res2d$mergedQual, rep(c(10L, 40L), c(4, 7)))
expect_identical(res2d$mergedLengths, 11L)
expect_identical(res2e$mergedSeq, "TTACAACACACA")
expect_identical(res2e$mergedQual, rep(c(10L, 40L), c(5, 7)))
expect_identical(res2e$mergedLengths, 12L)
## invalid overlaps specified/overlaps modified internally
## minOverlap > lenF -> no valid overlap
res0a <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 8, 7, 9, 9, 1, FALSE)
expect_type(res0a, "list")
expect_identical(res0a$mergedSeq, sF2)
expect_identical(res0a$mergedQual, qF2)
expect_identical(res0a$mergedLengths, 7L)
expect_true(res0a$return)
## minOverlap = 0, lenF > lenR -> minOverlap = lenR
sF0 <- "TTACACG"; qF0 <- rep(10L, nchar(sF0)); lF0 <- nchar(sF0)
sR0 <- "ACACG"; qR0 <- rep(40L, nchar(sR0)); lR0 <- nchar(sR0)
res0b <- mutscan:::test_mergeReadPairPartial(sF0, qF0, sR0, qR0, lF0, lR0, 0, 7, 5, 9, 1, FALSE)
expect_type(res0b, "list")
expect_identical(res0b$mergedSeq, sF0)
expect_identical(res0b$mergedQual, rep(c(10L, 40L), c(2, 5)))
expect_identical(res0b$mergedLengths, 7L)
expect_false(res0b$return)
## maxOverlap = 0, lenF > lenR -> maxOverlap = lenR
res0c <- mutscan:::test_mergeReadPairPartial(sF0, qF0, sR0, qR0, lF0, lR0, 1, 0, 5, 9, 1, FALSE)
expect_type(res0c, "list")
expect_identical(res0c$mergedSeq, sF0)
expect_identical(res0c$mergedQual, rep(c(10L, 40L), c(2, 5)))
expect_identical(res0c$mergedLengths, 7L)
expect_false(res0c$return)
## minOverlap > maxOverlap -> no valid overlap
res0d <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 4, 3, 9, 9, 1, FALSE)
expect_type(res0d, "list")
expect_identical(res0d$mergedSeq, sF2)
expect_identical(res0d$mergedQual, qF2)
expect_identical(res0d$mergedLengths, 7L)
expect_true(res0d$return)
## padded reads
for (i in 1:10) {
sF <- paste(rep(c("C","A"), c(i, 6)), collapse = "")
qF <- rep(30L, nchar(sF))
sR <- paste(rep(c("A","C"), c(6, i)), collapse = "")
qR <- rep(30L, nchar(sR))
lF <- i + 6
lR <- 6 + i
res <- mutscan:::test_mergeReadPairPartial(sF, qF, sR, qR, lF, lR, 6, 6, 0, 0, 0)
expect_identical(res$mergedSeq, paste(rep(c("C","A","C"), c(i, 6, i)), collapse = ""))
expect_equal(res$mergedLengths, i + 6 + i)
}
## reads of unequal length
sR <- paste(rep("A", 6), collapse = "")
qR <- rep(30L, nchar(sR))
lR <- 6L
for (i in 1:10) {
sF <- paste(rep(c("C","A"), c(i, 6)), collapse = "")
qF <- rep(30L, nchar(sF))
lF <- i + 6
res <- mutscan:::test_mergeReadPairPartial(sF, qF, sR, qR, lF, lR, 6, 6, 0, 0, 0)
expect_identical(res$mergedSeq, sF)
expect_equal(res$mergedLengths, lF)
res <- mutscan:::test_mergeReadPairPartial(sR, qR, sF, qF, lR, lF, 6, 6, 0, 0, 0)
expect_identical(res$mergedSeq, sR)
expect_equal(res$mergedLengths, lR)
}
## test variable segment lengths merging
## ... that must work
sF3 <- "AAAAAAAAACGTCCCAAC"; qF3 <- rep(40L, nchar(sF3)); lF3 <- c(13L, 5L)
sR3 <- "CGTCCCAACCCGGGGGGGGG"; qR3 <- rep(42L, nchar(sR3)); lR3 <- c( 4L, 16L)
res3a <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, lF3, lR3, 1, 0, 1, 0, 0.1, FALSE)
res3b <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), 20L, 1, 0, 1, 0, 0.1, FALSE)
res3c <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), c(14L, 6L), 1, 0, 1, 0, 0.1, FALSE)
res3d <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 8L, 5L), c(4L, 13L, 3L), 1, 0, 1, 0, 0.1, FALSE)
res3e <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(3L, 2L, 8L, 2L, 3L), c(4L, 2L, 11L, 3L), 1, 0, 1, 0, 0.1, FALSE)
res3f <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), c(9L, 5L, 6L), 1, 0, 1, 0, 0.1, FALSE)
expect_false(res3a$return)
expect_identical(res3a$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3a$mergedLengths, c(13L, 16L))
expect_identical(res3b$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3b$mergedLengths, c(5L, 24L))
expect_identical(res3c$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3c$mergedLengths, c(5L, 18L, 6L))
expect_identical(res3d$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3d$mergedLengths, c(5L, 8L, 13L, 3L))
expect_identical(res3e$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3e$mergedLengths, c(3L, 2L, 8L, 2L, 11L, 3L))
expect_identical(res3f$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3f$mergedLengths, c(5L, 13L, 5L, 6L))
## ... that must fail
res3g <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(12L, 6L), c( 4L, 16L), 1, 0, 1, 0, 0.1, FALSE)
res3h <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), c(2L, 18L), 1, 0, 1, 0, 0.1, FALSE)
res3i <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(12L, 6L), c(3L, 4L, 2L, 11L), 1, 0, 1, 0, 0.1, FALSE)
expect_identical(res3g$mergedSeq, sF3)
expect_true(res3g$return)
expect_identical(res3h$mergedSeq, sF3)
expect_true(res3h$return)
expect_identical(res3i$mergedSeq, sF3)
expect_true(res3i$return)
## ... that completely overlaps and must work
res3j <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sF3, qF3, 18L, 18L, 1, 0, 1, 0, 0.1, FALSE)
res3k <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sF3, qF3, c(5L, 13L), c(5L, 13L), 1, 0, 1, 0, 0.1, FALSE)
expect_identical(res3j$mergedSeq, sF3)
expect_false(res3j$return)
expect_equal(res3j$mergedLengths, 18L)
expect_identical(res3k$mergedSeq, sF3)
expect_false(res3k$return)
expect_equal(res3k$mergedLengths, c(5L, 13L))
})
## ----------------------------------------------------------------------------
## makeBaseHGVS/makeAAHGVS
## ----------------------------------------------------------------------------
test_that("makeBaseHGVS works", {
expect_equal(makeBaseHGVS(c("FOS.1.A", "FOS.2.T"), ".", "TAG", "ATG"), "1_2delinsAT_")
expect_equal(makeBaseHGVS(c("f.1.A", "r.4.A"), ".", "TAGT", "AAGA"), "[1T>A;4T>A]_")
expect_equal(makeBaseHGVS(c("f.1.A", "r.4.A", "f.6.C"), ".", "TAGTGTAGTCCGT", "AAGAGCAGTCCGT"),
"[1T>A;4_6delinsAGC]_")
expect_equal(makeBaseHGVS(c("r.4.A"), ".", "TAGTGTAGTCCGT", "TAGAGTAGTCCGT"), "4T>A_")
})
test_that("makeAAHGVS works", {
expect_equal(test_makeAAHGVS("FOS.1.H", ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"(Thr1His)_")
expect_equal(test_makeAAHGVS(c("f.1.L", "r.4.M"), ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"[(Thr1Leu);(Leu4Met)]_")
expect_equal(test_makeAAHGVS(c("f.1.L", "f.2.M"), ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"[(Thr1Leu);(Asp2Met)]_")
expect_equal(test_makeAAHGVS(c("f.1.L", "f.2.M", "f.7.M"), ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"[(Thr1Leu);(Asp2Met);(Glu7Met)]_")
})
fmicompbio/mutscan documentation built on Oct. 24, 2024, 2:41 p.m.
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## ----------------------------------------------------------------------------
## compareCodonPositions
## ----------------------------------------------------------------------------
test_that("compareCodonPositions works", {
expect_true(compareCodonPositions("f.1.AAA_", "f.2.ACT_", "."))
expect_true(compareCodonPositions("f.2.ACT_", "f.10.TCA_", "."))
})
## ----------------------------------------------------------------------------
## findClosestRefSeq
## ----------------------------------------------------------------------------
test_that("findClosestRefSeq works", {
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ACGT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 0L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ACG", "ACGT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("AACGT", "ACCTA"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 0L, sim = 0L), -1L)
expect_equal(findClosestRefSeq(varSeq = "ACGT", wtSeq = c("ATGT", "ACTT"),
upperBoundMismatch = 1L, sim = 0L), -2L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ACGT", "ACTT"),
upperBoundMismatch = 4L, sim = 0L), 0L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ACG", "ACGT"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("AACGT", "ACCTA"),
upperBoundMismatch = 4L, sim = 0L), 1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ATTT", "ACTT"),
upperBoundMismatch = 0L, sim = 0L), -1L)
expect_equal(findClosestRefSeqEarlyStop(varSeq = "ACGT", wtSeq = c("ATGT", "ACTT"),
upperBoundMismatch = 1L, sim = 0L), -2L)
})
## ----------------------------------------------------------------------------
## decomposeRead
## ----------------------------------------------------------------------------
test_that("decomposeRead works", {
## All element lengths specified, no primer
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVCUSV",
elementLengths = c(2, 1, 3, 3, 1, 2, 1, 1), primerSeqs = "",
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "", nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACCT")
expect_equal(res$varSeq, "AAGG")
expect_equal(res$varQual, "gABG")
expect_equal(res$varLengths, c(3L, 1L))
expect_equal(res$constSeq, "TTAC")
expect_equal(res$constQual, "defC")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## All element lengths specified, no primer, 0 lengths included
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTG", squal = "abcdefgABCDEF", elements = "SUSCVUCUS",
elementLengths = c(0, 2, 1, 3, 3, 0, 1, 2, 1), primerSeqs = "",
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACCT")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTAC")
expect_equal(res$constQual, "defC")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Derive variable length from other lengths
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTG", squal = "abcdefgABCDEF", elements = "USCVCUS",
elementLengths = c(2, 1, 3, -1, 1, 2, 1), primerSeqs = "",
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACCT")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTAC")
expect_equal(res$constQual, "defC")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVPS",
elementLengths = c(2, 1, 3, 3, 3, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Only variable sequence
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "V",
elementLengths = -1, primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "ACGTTAAAGCCTGG")
expect_equal(res$varQual, "abcdefgABCDEFG")
expect_equal(res$varLengths, 14L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer + variable sequence
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "PV",
elementLengths = c(-1, -1), primerSeqs = c("ACG"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "TTAAAGCCTGG")
expect_equal(res$varQual, "defgABCDEFG")
expect_equal(res$varLengths, 11L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Variable sequence + primer
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VP",
elementLengths = c(-1, -1), primerSeqs = c("ACG"),
varSeq = "A", varQual = "E", varLengths = 1L, umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "A")
expect_equal(res$varQual, "E")
expect_equal(res$varLengths, c(1L, 0L))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer, not the right length of sequence
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VPU",
elementLengths = c(10, 3, 2), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0L), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 1)
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VPU",
elementLengths = c(8, 3, 2), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 1)
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "CVPU",
elementLengths = c(10, -1, 3, 2), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 1)
## Primer, but don't explicitly specify that the part after the primer should be skipped
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Multiple primers, only one present
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("TTT", "CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Multiple primers, none present
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("TTT", "GGG"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "")
expect_equal(res$varQual, "")
expect_equal(res$varLengths, integer(0))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 1)
expect_equal(res$nReadWrongLength, 0)
## Multiple primers, all present (use the first one)
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "USCVP",
elementLengths = c(2, 1, 3, 3, 3), primerSeqs = c("CCT", "TTA"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "AC")
expect_equal(res$varSeq, "AAG")
expect_equal(res$varQual, "gAB")
expect_equal(res$varLengths, 3L)
expect_equal(res$constSeq, "TTA")
expect_equal(res$constQual, "def")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer, infer length of sequences
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "UPV",
elementLengths = c(-1, 3, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACGTTAAAG")
expect_equal(res$varSeq, "GG")
expect_equal(res$varQual, "FG")
expect_equal(res$varLengths, 2L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Primer, don't specify primer length
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "UPV",
elementLengths = c(-1, -1, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "ACGTTAAAG")
expect_equal(res$varSeq, "GG")
expect_equal(res$varQual, "FG")
expect_equal(res$varLengths, 2L)
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
## Multiple variable segments with different lengths
res <- mutscan:::test_decomposeRead(
sseq = "ACGTTAAAGCCTGG", squal = "abcdefgABCDEFG", elements = "VPV",
elementLengths = c(-1, -1, -1), primerSeqs = c("CCT"),
varSeq = "", varQual = "", varLengths = integer(0), umiSeq = "",
constSeq = "", constQual = "",
nNoPrimer = 0, nReadWrongLength = 0)
expect_equal(res$umiSeq, "")
expect_equal(res$varSeq, "ACGTTAAAGGG")
expect_equal(res$varQual, "abcdefgABFG")
expect_equal(res$varLengths, c(9L, 2L))
expect_equal(res$constSeq, "")
expect_equal(res$constQual, "")
expect_equal(res$nNoPrimer, 0)
expect_equal(res$nReadWrongLength, 0)
})
## ----------------------------------------------------------------------------
## mergeReadPairsPartial
## ----------------------------------------------------------------------------
test_that("mergeReadPairsPartial works", {
## don't count N as mismatch, pick base with higher quality
sF1 <- "AAAANA"; qF1 <- rep(40L, nchar(sF1)); lF1 <- 6L
sR1 <- "AACCCC"; qR1 <- rep(42L, nchar(sR1)); lR1 <- 6L
res1a <- mutscan:::test_mergeReadPairPartial(sF1, qF1, sR1, qR1, lF1, lR1, 1, 6, 0, 0, 1/4, TRUE)
res1b <- mutscan:::test_mergeReadPairPartial(sF1, qF1, sR1, qR1, lF1, lR1, 1, 6, 0, 0, 1/4, FALSE)
res1c <- mutscan:::test_mergeReadPairPartial(sF1, qR1, sR1, qF1, lF1, lR1, 2, 2, 0, 0, 1/4, TRUE)
res1d <- mutscan:::test_mergeReadPairPartial(sF1, qF1, sR1, qR1, lF1, lR1, 2, 2, 0, 0, 0, TRUE)
expect_type(res1a, "list")
expect_type(res1b, "list")
expect_type(res1c, "list")
expect_type(res1d, "list")
expect_identical(res1a$mergedSeq, "AAAACCCC")
expect_identical(res1a$mergedQual, rep(c(40L, 42L), c(2, 6)))
expect_identical(res1a$mergedLengths, 8L)
expect_identical(res1a, res1b)
expect_identical(res1c$mergedSeq, "AAAANACCCC")
expect_identical(res1d$mergedSeq, "AAAAAACCCC")
expect_identical(res1c$mergedLengths, 10L)
expect_identical(res1d$mergedLengths, 10L)
## no valid overlap, multiple possible overlaps with single mismatch
sF2 <- "TTACACG"; qF2 <- rep(10L, nchar(sF2)); lF2 <- 7L
sR2 <- "ACACACA"; qR2 <- rep(40L, nchar(sR2)); lR2 <- 7L
res2a <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 0, 0, 0, 0, maxFracMismatchOverlap = 3/7, TRUE)
res2b <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 0, 0, 1/5, TRUE)
expect_type(res2a, "list")
expect_type(res2b, "list")
expect_identical(res2a$mergedSeq, sR2)
expect_identical(res2a$mergedQual, qR2)
expect_identical(res2a$mergedLengths, 7L)
expect_identical(res2b$mergedSeq, "TTACACACA")
expect_identical(res2b$mergedQual, rep(c(10L,40L), c(2,7)))
expect_identical(res2b$mergedLengths, 9L)
## specify min/max merged length instead
res2c <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 9, 9, 1, FALSE)
res2d <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 11, 11, 1, FALSE)
res2e <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 12, 12, 1, FALSE)
expect_type(res2c, "list")
expect_type(res2d, "list")
expect_type(res2e, "list")
expect_identical(res2c$mergedSeq, "TTACACACA")
expect_identical(res2c$mergedQual, rep(c(10L, 40L), c(2, 7)))
expect_identical(res2c$mergedLengths, 9L)
expect_identical(res2d$mergedSeq, "TTACACACACA")
expect_identical(res2d$mergedQual, rep(c(10L, 40L), c(4, 7)))
expect_identical(res2d$mergedLengths, 11L)
expect_identical(res2e$mergedSeq, "TTACAACACACA")
expect_identical(res2e$mergedQual, rep(c(10L, 40L), c(5, 7)))
expect_identical(res2e$mergedLengths, 12L)
## invalid overlaps specified/overlaps modified internally
## minOverlap > lenF -> no valid overlap
res0a <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 8, 7, 9, 9, 1, FALSE)
expect_type(res0a, "list")
expect_identical(res0a$mergedSeq, sF2)
expect_identical(res0a$mergedQual, qF2)
expect_identical(res0a$mergedLengths, 7L)
expect_true(res0a$return)
## minOverlap = 0, lenF > lenR -> minOverlap = lenR
sF0 <- "TTACACG"; qF0 <- rep(10L, nchar(sF0)); lF0 <- nchar(sF0)
sR0 <- "ACACG"; qR0 <- rep(40L, nchar(sR0)); lR0 <- nchar(sR0)
res0b <- mutscan:::test_mergeReadPairPartial(sF0, qF0, sR0, qR0, lF0, lR0, 0, 7, 5, 9, 1, FALSE)
expect_type(res0b, "list")
expect_identical(res0b$mergedSeq, sF0)
expect_identical(res0b$mergedQual, rep(c(10L, 40L), c(2, 5)))
expect_identical(res0b$mergedLengths, 7L)
expect_false(res0b$return)
## maxOverlap = 0, lenF > lenR -> maxOverlap = lenR
res0c <- mutscan:::test_mergeReadPairPartial(sF0, qF0, sR0, qR0, lF0, lR0, 1, 0, 5, 9, 1, FALSE)
expect_type(res0c, "list")
expect_identical(res0c$mergedSeq, sF0)
expect_identical(res0c$mergedQual, rep(c(10L, 40L), c(2, 5)))
expect_identical(res0c$mergedLengths, 7L)
expect_false(res0c$return)
## minOverlap > maxOverlap -> no valid overlap
res0d <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 4, 3, 9, 9, 1, FALSE)
expect_type(res0d, "list")
expect_identical(res0d$mergedSeq, sF2)
expect_identical(res0d$mergedQual, qF2)
expect_identical(res0d$mergedLengths, 7L)
expect_true(res0d$return)
## padded reads
for (i in 1:10) {
sF <- paste(rep(c("C","A"), c(i, 6)), collapse = "")
qF <- rep(30L, nchar(sF))
sR <- paste(rep(c("A","C"), c(6, i)), collapse = "")
qR <- rep(30L, nchar(sR))
lF <- i + 6
lR <- 6 + i
res <- mutscan:::test_mergeReadPairPartial(sF, qF, sR, qR, lF, lR, 6, 6, 0, 0, 0)
expect_identical(res$mergedSeq, paste(rep(c("C","A","C"), c(i, 6, i)), collapse = ""))
expect_equal(res$mergedLengths, i + 6 + i)
}
## reads of unequal length
sR <- paste(rep("A", 6), collapse = "")
qR <- rep(30L, nchar(sR))
lR <- 6L
for (i in 1:10) {
sF <- paste(rep(c("C","A"), c(i, 6)), collapse = "")
qF <- rep(30L, nchar(sF))
lF <- i + 6
res <- mutscan:::test_mergeReadPairPartial(sF, qF, sR, qR, lF, lR, 6, 6, 0, 0, 0)
expect_identical(res$mergedSeq, sF)
expect_equal(res$mergedLengths, lF)
res <- mutscan:::test_mergeReadPairPartial(sR, qR, sF, qF, lR, lF, 6, 6, 0, 0, 0)
expect_identical(res$mergedSeq, sR)
expect_equal(res$mergedLengths, lR)
}
## test variable segment lengths merging
## ... that must work
sF3 <- "AAAAAAAAACGTCCCAAC"; qF3 <- rep(40L, nchar(sF3)); lF3 <- c(13L, 5L)
sR3 <- "CGTCCCAACCCGGGGGGGGG"; qR3 <- rep(42L, nchar(sR3)); lR3 <- c( 4L, 16L)
res3a <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, lF3, lR3, 1, 0, 1, 0, 0.1, FALSE)
res3b <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), 20L, 1, 0, 1, 0, 0.1, FALSE)
res3c <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), c(14L, 6L), 1, 0, 1, 0, 0.1, FALSE)
res3d <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 8L, 5L), c(4L, 13L, 3L), 1, 0, 1, 0, 0.1, FALSE)
res3e <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(3L, 2L, 8L, 2L, 3L), c(4L, 2L, 11L, 3L), 1, 0, 1, 0, 0.1, FALSE)
res3f <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), c(9L, 5L, 6L), 1, 0, 1, 0, 0.1, FALSE)
expect_false(res3a$return)
expect_identical(res3a$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3a$mergedLengths, c(13L, 16L))
expect_identical(res3b$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3b$mergedLengths, c(5L, 24L))
expect_identical(res3c$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3c$mergedLengths, c(5L, 18L, 6L))
expect_identical(res3d$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3d$mergedLengths, c(5L, 8L, 13L, 3L))
expect_identical(res3e$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3e$mergedLengths, c(3L, 2L, 8L, 2L, 11L, 3L))
expect_identical(res3f$mergedSeq, "AAAAAAAAACGTCCCAACCCGGGGGGGGG")
expect_equal(res3f$mergedLengths, c(5L, 13L, 5L, 6L))
## ... that must fail
res3g <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(12L, 6L), c( 4L, 16L), 1, 0, 1, 0, 0.1, FALSE)
res3h <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(5L, 13L), c(2L, 18L), 1, 0, 1, 0, 0.1, FALSE)
res3i <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sR3, qR3, c(12L, 6L), c(3L, 4L, 2L, 11L), 1, 0, 1, 0, 0.1, FALSE)
expect_identical(res3g$mergedSeq, sF3)
expect_true(res3g$return)
expect_identical(res3h$mergedSeq, sF3)
expect_true(res3h$return)
expect_identical(res3i$mergedSeq, sF3)
expect_true(res3i$return)
## ... that completely overlaps and must work
res3j <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sF3, qF3, 18L, 18L, 1, 0, 1, 0, 0.1, FALSE)
res3k <- mutscan:::test_mergeReadPairPartial(sF3, qF3, sF3, qF3, c(5L, 13L), c(5L, 13L), 1, 0, 1, 0, 0.1, FALSE)
expect_identical(res3j$mergedSeq, sF3)
expect_false(res3j$return)
expect_equal(res3j$mergedLengths, 18L)
expect_identical(res3k$mergedSeq, sF3)
expect_false(res3k$return)
expect_equal(res3k$mergedLengths, c(5L, 13L))
})
## ----------------------------------------------------------------------------
## makeBaseHGVS/makeAAHGVS
## ----------------------------------------------------------------------------
test_that("makeBaseHGVS works", {
expect_equal(makeBaseHGVS(c("FOS.1.A", "FOS.2.T"), ".", "TAG", "ATG"), "1_2delinsAT_")
expect_equal(makeBaseHGVS(c("f.1.A", "r.4.A"), ".", "TAGT", "AAGA"), "[1T>A;4T>A]_")
expect_equal(makeBaseHGVS(c("f.1.A", "r.4.A", "f.6.C"), ".", "TAGTGTAGTCCGT", "AAGAGCAGTCCGT"),
"[1T>A;4_6delinsAGC]_")
expect_equal(makeBaseHGVS(c("r.4.A"), ".", "TAGTGTAGTCCGT", "TAGAGTAGTCCGT"), "4T>A_")
})
test_that("makeAAHGVS works", {
expect_equal(test_makeAAHGVS("FOS.1.H", ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"(Thr1His)_")
expect_equal(test_makeAAHGVS(c("f.1.L", "r.4.M"), ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"[(Thr1Leu);(Leu4Met)]_")
expect_equal(test_makeAAHGVS(c("f.1.L", "f.2.M"), ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"[(Thr1Leu);(Asp2Met)]_")
expect_equal(test_makeAAHGVS(c("f.1.L", "f.2.M", "f.7.M"), ".", "TDTLQAETDQLEDEKSALQTEIANLLKEKEKL"),
"[(Thr1Leu);(Asp2Met);(Glu7Met)]_")
})
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