tests/testthat/test_digestFastqs_parallelization.R
In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data
test_that("parallel processing works (cis)", {
fqc1 <- system.file("extdata/cisInput_1.fastq.gz", package = "mutscan")
fqc2 <- system.file("extdata/cisInput_2.fastq.gz", package = "mutscan")
## default arguments
Ldef <- list(
fastqForward = fqc1, fastqReverse = fqc2,
mergeForwardReverse = TRUE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 1, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = TRUE,
elementsForward = "SUCV", elementsReverse = "SUCVS",
elementLengthsForward = c(1, 10, 18, 96),
elementLengthsReverse = c(1, 7, 17, 96, -1),
adapterForward = "GGAAGAGCACACGTC",
adapterReverse = "GGAAGAGCGTCGTGT",
primerForward = "",
primerReverse = "",
wildTypeForward = c(wt1 = "ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wt2 = "CCTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wt3 = "ACTGATACACTCCAAGCGGAGACTGACCAACTAGAAGATGAGAAGTCTTCTTTGCAGACCGAGATTGCCAACGTGCTGAAGGAGAAGGAAAAACTA"),
wildTypeReverse = "",
constantForward = "AACCGGAGGAGGGAGCTG",
constantReverse = "GAGTTCATCCTGGCAGC",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = -1,
nbrMutatedCodonsMaxReverse = -1,
nbrMutatedBasesMaxForward = 2,
nbrMutatedBasesMaxReverse = 2,
forbiddenMutatedCodonsForward = "NNW",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1,
maxReadLength = 1024
)
res <- do.call(digestFastqs, Ldef)
## Increase number of threads
Ldef1 <- Ldef; Ldef1$nThreads <- 3
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## Increase chunk size
Ldef1 <- Ldef; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## With tree matching
Ldef1 <- Ldef; Ldef1$useTreeWTmatch <- TRUE; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
})
test_that("parallel processing works (trans)", {
fqt1 <- system.file("extdata/transInput_1.fastq.gz", package = "mutscan")
fqt2 <- system.file("extdata/transInput_2.fastq.gz", package = "mutscan")
## default arguments
Ldef <- list(
fastqForward = fqt1, fastqReverse = fqt2,
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SUCV", elementsReverse = "SUCV",
elementLengthsForward = c(1, 10, 18, 96),
elementLengthsReverse = c(1, 8, 20, 96),
adapterForward = "GGAAGAGCACACGTC",
adapterReverse = "GGAAGAGCGTCGTGT",
primerForward = "",
primerReverse = "",
wildTypeForward = "ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "AACCGGAGGAGGGAGCTG",
constantReverse = "GAAAAAGGAAGCTGGAGAGA",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 1,
nbrMutatedCodonsMaxReverse = 1,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "NNW",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1,
maxReadLength = 1024
)
res <- do.call(digestFastqs, Ldef)
## Increase number of threads
Ldef1 <- Ldef; Ldef1$nThreads <- 3
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## Increase chunk size
Ldef1 <- Ldef; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## With tree matching
Ldef1 <- Ldef; Ldef1$useTreeWTmatch <- TRUE; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
})
fmicompbio/mutscan documentation built on March 30, 2024, 9:13 a.m.
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test_that("parallel processing works (cis)", {
fqc1 <- system.file("extdata/cisInput_1.fastq.gz", package = "mutscan")
fqc2 <- system.file("extdata/cisInput_2.fastq.gz", package = "mutscan")
## default arguments
Ldef <- list(
fastqForward = fqc1, fastqReverse = fqc2,
mergeForwardReverse = TRUE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 1, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = TRUE,
elementsForward = "SUCV", elementsReverse = "SUCVS",
elementLengthsForward = c(1, 10, 18, 96),
elementLengthsReverse = c(1, 7, 17, 96, -1),
adapterForward = "GGAAGAGCACACGTC",
adapterReverse = "GGAAGAGCGTCGTGT",
primerForward = "",
primerReverse = "",
wildTypeForward = c(wt1 = "ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wt2 = "CCTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wt3 = "ACTGATACACTCCAAGCGGAGACTGACCAACTAGAAGATGAGAAGTCTTCTTTGCAGACCGAGATTGCCAACGTGCTGAAGGAGAAGGAAAAACTA"),
wildTypeReverse = "",
constantForward = "AACCGGAGGAGGGAGCTG",
constantReverse = "GAGTTCATCCTGGCAGC",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = -1,
nbrMutatedCodonsMaxReverse = -1,
nbrMutatedBasesMaxForward = 2,
nbrMutatedBasesMaxReverse = 2,
forbiddenMutatedCodonsForward = "NNW",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1,
maxReadLength = 1024
)
res <- do.call(digestFastqs, Ldef)
## Increase number of threads
Ldef1 <- Ldef; Ldef1$nThreads <- 3
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## Increase chunk size
Ldef1 <- Ldef; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## With tree matching
Ldef1 <- Ldef; Ldef1$useTreeWTmatch <- TRUE; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
})
test_that("parallel processing works (trans)", {
fqt1 <- system.file("extdata/transInput_1.fastq.gz", package = "mutscan")
fqt2 <- system.file("extdata/transInput_2.fastq.gz", package = "mutscan")
## default arguments
Ldef <- list(
fastqForward = fqt1, fastqReverse = fqt2,
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SUCV", elementsReverse = "SUCV",
elementLengthsForward = c(1, 10, 18, 96),
elementLengthsReverse = c(1, 8, 20, 96),
adapterForward = "GGAAGAGCACACGTC",
adapterReverse = "GGAAGAGCGTCGTGT",
primerForward = "",
primerReverse = "",
wildTypeForward = "ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "AACCGGAGGAGGGAGCTG",
constantReverse = "GAAAAAGGAAGCTGGAGAGA",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 1,
nbrMutatedCodonsMaxReverse = 1,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "NNW",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = 0,
constantMaxDistReverse = 0,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1,
maxReadLength = 1024
)
res <- do.call(digestFastqs, Ldef)
## Increase number of threads
Ldef1 <- Ldef; Ldef1$nThreads <- 3
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## Increase chunk size
Ldef1 <- Ldef; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
## With tree matching
Ldef1 <- Ldef; Ldef1$useTreeWTmatch <- TRUE; Ldef1$nThreads <- 3; Ldef1$chunkSize <- 100
## Capture warnings from missing OpenMP/not enough threads
a <- capture_warnings({
res1 <- do.call(digestFastqs, Ldef1)
})
expect_equal(sum(grepl("OpenMP|available", a)), length(a))
expect_equal(res$filterSummary$nbrTotal, res1$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res1$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res1$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res1$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res1$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res1$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res1$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res1$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res1$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res1$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res1$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res1$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res1$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res1$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res1$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res1$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res1$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res1$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res1$summaryTable$sequence)
})
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