tests/testthat/test_import.R
In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics
context("import")
test_that(".listTopDownFiles", {
fns <- tempfile(pattern=c("fileA_", "fileB_"))
fasta <- tempfile(pattern="fileA_", fileext=".fasta")
fns <- paste(rep(fns, each=3), c("experiments.csv", "mzML", "txt"),
sep=".")
file.create(c(fasta, fns))
fns <- normalizePath(fns)
fasta <- normalizePath(fasta)
r <- split(fns, c("csv", "mzML", "txt"))
r$fasta <- fasta
r <- r[order(names(r))]
expect_equal(.listTopDownFiles(tempdir()), r)
expect_equal(.listTopDownFiles(tempdir(), pattern="^fileA_.*"),
lapply(r, "[", 1L))
expect_error(.listTopDownFiles(tempdir(), pattern="^fileB_.*"),
"Could not find any fasta files")
expect_error(.listTopDownFiles(tempdir(), pattern="^fileC_.*"),
"Could not find any csv, fasta, mzML, txt files")
fasta2 <- tempfile(pattern="fileB_", fileext=".fasta")
file.create(fasta2)
expect_error(.listTopDownFiles(tempdir()),
"More than one fasta file")
fns2 <- tempfile("fileA_")
fns2 <- paste(fns2, c("mzML", "txt"), sep=".")
file.create(fns2)
expect_error(.listTopDownFiles(tempdir(), pattern="^fileA_.*"),
paste0("There have to be the same number .*",
"Found: csv=1, mzML=2, txt=2", collapse=""))
unlink(c(fasta, fasta2, fns, fns2))
})
test_that(".readExperimentCsv", {
fn <- paste0(tempfile(), ".experiments.csv")
d <- data.frame(MSLevel=c(1, 2, 2),
NaColumn=c("", "N/A", "NA"),
TargetedMassList=paste0("(mz=933.100", 1:3, " z=2 name=)"),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_message(e <- .readExperimentCsv(fn, verbose=TRUE),
"Reading 3 experiment conditions from file")
expect_equal(colnames(e),
c("MsLevel", "NaColumn", "TargetedMassList", "Condition",
"Mz", "File"))
expect_equal(e$MsLevel, rep(2, 2))
expect_equal(e$NaColumn, rep(NA, 2))
expect_equal(e$Condition, 1:2)
expect_equal(e$Mz, rep(933.1, 2))
expect_equal(e$File, rep(gsub("\\.experiments.csv", "", basename(fn)), 2))
unlink(fn)
})
test_that(".readFasta", {
fn <- paste0(tempfile(), ".fasta")
writeLines(c("> FOOBAR", "Sequence"), fn)
expect_message(s <- .readFasta(fn, verbose=TRUE),
"Reading sequence from fasta file")
expect_equal(s, AAString("Sequence"))
writeLines(c("> FOOBAR", "> Sequence"), fn)
expect_error(.readFasta(fn), "No sequence found")
unlink(fn)
})
test_that(".readScanHeadsTable", {
fn <- paste0(tempfile(), ".txt")
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0007@cid",
"ms2 100.0009@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
on.exit(unlink(fn))
expect_message(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=TRUE),
"Reading 5 header information from file")
expect_equal(colnames(h),
c("MsOrder", "FilterString", "Activation1", "Activation2",
"Energy1", "Energy2", "Condition",
"EtdActivation", "CidActivation", "HcdActivation",
"UvpdActivation", "Activation", "File"))
expect_equal(h$MsOrder, rep(2, 4))
expect_equal(h$EtdActivation, c(50, 50, NA, NA))
expect_equal(h$CidActivation, c(NA, NA, 20, 20))
expect_equal(h$HcdActivation, c(30, 30, NA, 10))
expect_equal(h$Condition, c(1, 1, 7, 9))
expect_equal(h$File, rep(gsub("\\.txt$", "", basename(fn)), 4))
## .fixFilterString needed
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0001@cid",
"ms2 100.0003@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_warning(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=TRUE),
"1 FilterString entries modified")
expect_equal(h$Condition, c(1, 1:3))
## .fixFilterString needed;
## https://github.com/sgibb/topdownr/issues/25
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0001@cid",
"ms2 100.0003@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_warning(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=TRUE),
"1 FilterString entries modified")
expect_equal(h$Condition, c(1, 1:3))
## duplicated IDs in different order (missing scans files)
## https://github.com/sgibb/topdownr/issues/14
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0007@cid",
"ms2 100.0001@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
ScanDescription=paste0("C0", c(1, 1:4)),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_warning(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=FALSE),
"not sorted in ascending order")
expect_equal(h$Condition, c(1, 1:3))
## test conditions argument
expect_error(.readScanHeadsTable(
fn, conditions="FOO", verbose=FALSE),
"should be one of .*FilterString.*")
expect_error(.readScanHeadsTable(
fn, conditions=TRUE, verbose=FALSE),
"'conditions' has to be a 'character' or 'numeric'")
expect_error(.readScanHeadsTable(
fn, conditions=1:2, verbose=FALSE),
"'conditions' has to be a 'character' or 'numeric'")
expect_warning(h <- .readScanHeadsTable(
fn, conditions="FilterString", verbose=FALSE),
"not sorted in ascending order")
expect_equal(h$Condition, c(1, 1:3))
expect_equal(.readScanHeadsTable(
fn, conditions="ScanDescription", verbose=FALSE)$Condition, 1:4)
expect_equal(.readScanHeadsTable(
fn, conditions=4, verbose=FALSE)$Condition, 1:4)
expect_equal(.readScanHeadsTable(
fn, conditions=2, verbose=FALSE)$Condition, c(1:2, 1:2))
})
test_that(".readSpectrum", {
expect_error(.readSpectrum(tempfile()), "File .* not found")
skip_if_not_installed("topdownrdata", "0.2")
f <- file.path(topdownrdata::topDownDataPath("myoglobin"),
"mzml", "myo_1211_ETDReagentTarget_1e6_1.mzML.gz")
expect_error(.readSpectrum(f, 0L), "Invalid .* 1:351")
expect_error(.readSpectrum(f, 1e3L), "Invalid .* 1:351")
expect_equal(.readSpectrum(f, 1L),
matrix(
c(16941.06087, 18979506.00),
nrow=1, dimnames = list(c(), c("mz", "intensity"))
)
)
})
test_that(".mergeScanConditionAndHeaderInformation", {
sc <- data.frame(FOO=1:3, Condition=c(1:2, 1), Both=1,
File=c("foo", "foo", "bar"),
CidActivation=1:3,
HcdActivation=NA,
Energy2=1:3)
hi <- data.frame(BAR=1:5, Condition=c(1, 1, 2, 2, 1), Both=2,
File=c("bar", "bar", "bar", "foo", "foo"),
SupplementalActivationCe=c(3, 3, 3, 2:1))
r <- data.frame(File=rep(c("bar", "foo"), each=2),
Condition=c(1, 1, 1, 2), FOO=c(3, 3, 1, 2),
Both.ScanCondition=c(1, 1, 1, 1),
CidActivation=c(3, 3, 1:2),
HcdActivation=NA,
Energy2=c(3, 3, 1:2),
BAR=c(1:2, 5:4),
Both.HeaderInformation=2,
SupplementalActivationCe=c(3, 3, 1, 2))
expect_equal(.mergeScanConditionAndHeaderInformation(sc, hi), r)
sc$CidActivation <- 0
sc$HcdActivation <- 11:13
expect_error(.mergeScanConditionAndHeaderInformation(sc, hi),
"Merging of header and method information failed")
})
test_that(".mergeSpectraAndHeaderInformation", {
fd <- data.frame(x=1:2, Scan=1:2, File="foo", spectrum=1:2, z=1:2,
RetentionTime=1:2)
hi <- data.frame(File="foo", Scan=1:2, y=3:4, z=3:4, RtMin=1:2,
stringsAsFactors=FALSE)
expect_error(.mergeSpectraAndHeaderInformation(fd, hi),
"The retention times .* differ.")
fd$RetentionTime <- (1:2) * 60
r <- fd
r$Scan <- 1:2
r$y <- 3:4
r$z.SpectraInformation <- r$z
r$z.HeaderInformation <- 3:4
r$RtMin <- 1:2
r <- r[, c("File", "Scan", "x", "spectrum",
"z.SpectraInformation", "RetentionTime",
"y", "z.HeaderInformation", "RtMin")]
expect_equal(.mergeSpectraAndHeaderInformation(fd, hi), r)
})
sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.
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context("import")
test_that(".listTopDownFiles", {
fns <- tempfile(pattern=c("fileA_", "fileB_"))
fasta <- tempfile(pattern="fileA_", fileext=".fasta")
fns <- paste(rep(fns, each=3), c("experiments.csv", "mzML", "txt"),
sep=".")
file.create(c(fasta, fns))
fns <- normalizePath(fns)
fasta <- normalizePath(fasta)
r <- split(fns, c("csv", "mzML", "txt"))
r$fasta <- fasta
r <- r[order(names(r))]
expect_equal(.listTopDownFiles(tempdir()), r)
expect_equal(.listTopDownFiles(tempdir(), pattern="^fileA_.*"),
lapply(r, "[", 1L))
expect_error(.listTopDownFiles(tempdir(), pattern="^fileB_.*"),
"Could not find any fasta files")
expect_error(.listTopDownFiles(tempdir(), pattern="^fileC_.*"),
"Could not find any csv, fasta, mzML, txt files")
fasta2 <- tempfile(pattern="fileB_", fileext=".fasta")
file.create(fasta2)
expect_error(.listTopDownFiles(tempdir()),
"More than one fasta file")
fns2 <- tempfile("fileA_")
fns2 <- paste(fns2, c("mzML", "txt"), sep=".")
file.create(fns2)
expect_error(.listTopDownFiles(tempdir(), pattern="^fileA_.*"),
paste0("There have to be the same number .*",
"Found: csv=1, mzML=2, txt=2", collapse=""))
unlink(c(fasta, fasta2, fns, fns2))
})
test_that(".readExperimentCsv", {
fn <- paste0(tempfile(), ".experiments.csv")
d <- data.frame(MSLevel=c(1, 2, 2),
NaColumn=c("", "N/A", "NA"),
TargetedMassList=paste0("(mz=933.100", 1:3, " z=2 name=)"),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_message(e <- .readExperimentCsv(fn, verbose=TRUE),
"Reading 3 experiment conditions from file")
expect_equal(colnames(e),
c("MsLevel", "NaColumn", "TargetedMassList", "Condition",
"Mz", "File"))
expect_equal(e$MsLevel, rep(2, 2))
expect_equal(e$NaColumn, rep(NA, 2))
expect_equal(e$Condition, 1:2)
expect_equal(e$Mz, rep(933.1, 2))
expect_equal(e$File, rep(gsub("\\.experiments.csv", "", basename(fn)), 2))
unlink(fn)
})
test_that(".readFasta", {
fn <- paste0(tempfile(), ".fasta")
writeLines(c("> FOOBAR", "Sequence"), fn)
expect_message(s <- .readFasta(fn, verbose=TRUE),
"Reading sequence from fasta file")
expect_equal(s, AAString("Sequence"))
writeLines(c("> FOOBAR", "> Sequence"), fn)
expect_error(.readFasta(fn), "No sequence found")
unlink(fn)
})
test_that(".readScanHeadsTable", {
fn <- paste0(tempfile(), ".txt")
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0007@cid",
"ms2 100.0009@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
on.exit(unlink(fn))
expect_message(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=TRUE),
"Reading 5 header information from file")
expect_equal(colnames(h),
c("MsOrder", "FilterString", "Activation1", "Activation2",
"Energy1", "Energy2", "Condition",
"EtdActivation", "CidActivation", "HcdActivation",
"UvpdActivation", "Activation", "File"))
expect_equal(h$MsOrder, rep(2, 4))
expect_equal(h$EtdActivation, c(50, 50, NA, NA))
expect_equal(h$CidActivation, c(NA, NA, 20, 20))
expect_equal(h$HcdActivation, c(30, 30, NA, 10))
expect_equal(h$Condition, c(1, 1, 7, 9))
expect_equal(h$File, rep(gsub("\\.txt$", "", basename(fn)), 4))
## .fixFilterString needed
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0001@cid",
"ms2 100.0003@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_warning(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=TRUE),
"1 FilterString entries modified")
expect_equal(h$Condition, c(1, 1:3))
## .fixFilterString needed;
## https://github.com/sgibb/topdownr/issues/25
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0001@cid",
"ms2 100.0003@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_warning(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=TRUE),
"1 FilterString entries modified")
expect_equal(h$Condition, c(1, 1:3))
## duplicated IDs in different order (missing scans files)
## https://github.com/sgibb/topdownr/issues/14
d <- data.frame(MSOrder=c(1, 2, 2, 2, 2),
FilterString=c("ms2 100.0001@etd", "ms2 100.0001@hcd",
"ms2 100.0001@hcd", "ms2 100.0007@cid",
"ms2 100.0001@hcd"),
Activation1=c("ETD", "ETD", "ETD", "HCD", "CID"),
Activation2=c(NA, "HCD", "HCD", "CID", "HCD"),
Energy1=c(10, 50, 50, NA, 20),
Energy2=c(NA, 30, 30, 20, 10),
ScanDescription=paste0("C0", c(1, 1:4)),
stringsAsFactors=FALSE)
write.csv(d, file=fn, row.names=FALSE)
expect_warning(h <- .readScanHeadsTable(fn, conditions="FilterString",
verbose=FALSE),
"not sorted in ascending order")
expect_equal(h$Condition, c(1, 1:3))
## test conditions argument
expect_error(.readScanHeadsTable(
fn, conditions="FOO", verbose=FALSE),
"should be one of .*FilterString.*")
expect_error(.readScanHeadsTable(
fn, conditions=TRUE, verbose=FALSE),
"'conditions' has to be a 'character' or 'numeric'")
expect_error(.readScanHeadsTable(
fn, conditions=1:2, verbose=FALSE),
"'conditions' has to be a 'character' or 'numeric'")
expect_warning(h <- .readScanHeadsTable(
fn, conditions="FilterString", verbose=FALSE),
"not sorted in ascending order")
expect_equal(h$Condition, c(1, 1:3))
expect_equal(.readScanHeadsTable(
fn, conditions="ScanDescription", verbose=FALSE)$Condition, 1:4)
expect_equal(.readScanHeadsTable(
fn, conditions=4, verbose=FALSE)$Condition, 1:4)
expect_equal(.readScanHeadsTable(
fn, conditions=2, verbose=FALSE)$Condition, c(1:2, 1:2))
})
test_that(".readSpectrum", {
expect_error(.readSpectrum(tempfile()), "File .* not found")
skip_if_not_installed("topdownrdata", "0.2")
f <- file.path(topdownrdata::topDownDataPath("myoglobin"),
"mzml", "myo_1211_ETDReagentTarget_1e6_1.mzML.gz")
expect_error(.readSpectrum(f, 0L), "Invalid .* 1:351")
expect_error(.readSpectrum(f, 1e3L), "Invalid .* 1:351")
expect_equal(.readSpectrum(f, 1L),
matrix(
c(16941.06087, 18979506.00),
nrow=1, dimnames = list(c(), c("mz", "intensity"))
)
)
})
test_that(".mergeScanConditionAndHeaderInformation", {
sc <- data.frame(FOO=1:3, Condition=c(1:2, 1), Both=1,
File=c("foo", "foo", "bar"),
CidActivation=1:3,
HcdActivation=NA,
Energy2=1:3)
hi <- data.frame(BAR=1:5, Condition=c(1, 1, 2, 2, 1), Both=2,
File=c("bar", "bar", "bar", "foo", "foo"),
SupplementalActivationCe=c(3, 3, 3, 2:1))
r <- data.frame(File=rep(c("bar", "foo"), each=2),
Condition=c(1, 1, 1, 2), FOO=c(3, 3, 1, 2),
Both.ScanCondition=c(1, 1, 1, 1),
CidActivation=c(3, 3, 1:2),
HcdActivation=NA,
Energy2=c(3, 3, 1:2),
BAR=c(1:2, 5:4),
Both.HeaderInformation=2,
SupplementalActivationCe=c(3, 3, 1, 2))
expect_equal(.mergeScanConditionAndHeaderInformation(sc, hi), r)
sc$CidActivation <- 0
sc$HcdActivation <- 11:13
expect_error(.mergeScanConditionAndHeaderInformation(sc, hi),
"Merging of header and method information failed")
})
test_that(".mergeSpectraAndHeaderInformation", {
fd <- data.frame(x=1:2, Scan=1:2, File="foo", spectrum=1:2, z=1:2,
RetentionTime=1:2)
hi <- data.frame(File="foo", Scan=1:2, y=3:4, z=3:4, RtMin=1:2,
stringsAsFactors=FALSE)
expect_error(.mergeSpectraAndHeaderInformation(fd, hi),
"The retention times .* differ.")
fd$RetentionTime <- (1:2) * 60
r <- fd
r$Scan <- 1:2
r$y <- 3:4
r$z.SpectraInformation <- r$z
r$z.HeaderInformation <- 3:4
r$RtMin <- 1:2
r <- r[, c("File", "Scan", "x", "spectrum",
"z.SpectraInformation", "RetentionTime",
"y", "z.HeaderInformation", "RtMin")]
expect_equal(.mergeSpectraAndHeaderInformation(fd, hi), r)
})
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