Nothing
test.createTmpDir <- function(){
tmp1 <- HTSeqGenie:::createTmpDir()
checkTrue(file.exists(tmp1), "createTmpDir() creates temporary directory")
tmp2 <- HTSeqGenie:::createTmpDir()
checkTrue(file.exists(tmp1))
checkTrue(tmp1 != tmp2, "createTmpDir does return uniq dir names")
unlink(tmp2, recursive=TRUE)
unlink(tmp1, recursive=TRUE)
tmp3 <- HTSeqGenie:::createTmpDir(prefix='test123_')
checkTrue(file.exists(tmp3), "createTmpDir() works with a prefix")
unlink(tmp3, recursive=TRUE)
}
test.FastQStreamer.getReads.pefq <- function() {
## paired-end fastq
## setup test framework
config.update <- list(chunk_size=10)
setupTestFramework(config.filename="test-data/test_config.txt", config.update=config.update,
testname="test.FastQStreamer.getReads.pefq")
## init FastQStreamer
FastQStreamer.init(input_file=getConfig("input_file"), input_file2=getConfig("input_file2"),
chunk_size=getConfig.integer("chunk_size"))
## read 10 reads
lreads <- FastQStreamer.getReads()
checkEquals(length(lreads[[2]]), 10, "FastQStreamer.getReads() doesn't return 10 reads")
## release FastQStreamer
FastQStreamer.release()
}
test.FastQStreamer.getReads.truncated <- function() {
## paired-end fastq
## setup test framework
config.update <- list(chunk_size=500)
setupTestFramework(config.filename="test-data/test_config_single_end.txt", config.update=config.update,
testname="test.FastQStreamer.getReads.truncated")
## init FastQStreamer
FastQStreamer.init(input_file=getPackageFile("test-data/truncated.fastq.gz"),
chunk_size=getConfig.integer("chunk_size"))
## try to read 500 reads
lreads <- try(FastQStreamer.getReads(), silent=TRUE)
checkEquals(class(lreads), "try-error")
## release FastQStreamer
FastQStreamer.release()
}
test.FastQStreamer.getReads.pefq.subsample <- function() {
## paired-end fastq with subsample
## setup test framework
config.update <- list(chunk_size=100, subsample_nbreads=17)
setupTestFramework(config.filename="test-data/test_config.txt", config.update=config.update,
testname="test.FastQStreamer.getReads.pefq.subsample")
## init FastQStreamer
FastQStreamer.init(input_file=getConfig("input_file"), input_file2=getConfig("input_file2"),
chunk_size=getConfig.integer("chunk_size"),
subsample_nbreads=getConfig.integer("subsample_nbreads"))
## read 17 reads
lreads <- FastQStreamer.getReads()
checkEquals(length(lreads[[2]]), 17, "FastQStreamer.getReads() doesn't return 17 reads")
## release FastQStreamer
FastQStreamer.release()
lreads
}
test.FastQStreamer.subsampler.isdeterministic <- function() {
## check if the subsampler is deterministic
lreads1 <- test.FastQStreamer.getReads.pefq.subsample()
lreads2 <- test.FastQStreamer.getReads.pefq.subsample()
## convert to character strings
reads1 <- as.character(sread(lreads1[[1]]))
reads2 <- as.character(sread(lreads2[[1]]))
## check
checkEquals(reads1, reads2, "FastQStreamer is not deterministic")
}
test.FastQStreamer.getReads.segz <- function() {
## single-end fastq.gz
## setup test framework
config.update <- list(input_file="inst/test-data/reads.fastq.gz", chunk_size=10, quality_encoding="illumina1.8")
setupTestFramework(config.filename="test-data/test_config_single_end.txt", config.update=config.update,
testname="test.FastQStreamer.getReads.segz")
## init FastQStreamer
FastQStreamer.init(input_file=getConfig("input_file"), input_file2=getConfig("input_file2"),
chunk_size=getConfig.integer("chunk_size"))
## read 10 reads
lreads <- FastQStreamer.getReads()
checkEquals(length(lreads[[1]]), 10, "FastQStreamer.getReads() doesn't return 10 reads")
## release FastQStreamer
FastQStreamer.release()
}
test.writeAudit <- function() {
## setup test framework
config.filename <- "test-data/test_config.txt"
setupTestFramework(config.filename=config.filename, testname="test.writeAudit")
writeAudit("audit.txt")
}
test.safeUnlink <- function() {
tmpdir <- tempfile()
dir.create(tmpdir)
currentdir <- getwd()
setwd(tmpdir)
## create blob/tk and sblob linking to blob
system("mkdir blob ; touch blob/tk ; ln -s blob sblob")
## safeUnlink should not delete tk!
safeUnlink("sblob")
checkTrue(!file.exists("sblob"), "safeUnlink did not work!")
checkTrue(file.exists("blob/tk"), "safeUnlink did not work!")
setwd(currentdir)
}
test.detectQualityInFASTQFile <- function(){
tmpdir <- HTSeqGenie:::createTmpDir(prefix="test_detectQualityInFASTQFile")
file1 <- file.path(tmpdir, "1.fastq")
shortread1 <- ShortReadQ( DNAStringSet("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
quality = FastqQuality("!#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ"),
id = BStringSet("read_with_illumina1.8/1"))
writeFastq(shortread1, file=file1, lane='')
checkEquals(detectQualityInFASTQFile(file1), c("illumina1.8", "GATK-rescaled"))
unlink(file1)
shortread1 <- ShortReadQ( DNAStringSet("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
quality = FastqQuality(">BCBH@CAIF=B>&EFBFEBGEDHFII9HBDGHDHGFF@ICFBFBG>DGAH@KDIC1DAJ@KF?CAFBIGGBAB@C"),
id = BStringSet("read_with_rescaled_qual/1"))
writeFastq(shortread1, file=file1, lane='')
checkEquals(detectQualityInFASTQFile(file1), "GATK-rescaled")
unlink(file1)
shortread1 <- ShortReadQ( DNAStringSet("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
quality = FastqQuality("BCDEFGHIBCDEFGHIBCDEFGHIBCDEFGHIBCDEFGHIBCDEFGHI"),
id = BStringSet("read_with_all_quals/1"))
writeFastq(shortread1, file=file1, lane='')
checkEquals(detectQualityInFASTQFile(file1), c("solexa", "illumina1.3", "illumina1.5", "illumina1.8", "GATK-rescaled", "sanger"))
unlink(file1)
}
test.getObjectFilename <- function(){
expected = file.path(tempdir(), "AAA_BBB.tmp")
system(paste("touch ", expected, sep=" "))
observed = getObjectFilename(tempdir(), "AAA")
checkEquals(observed, expected, "getObjectFilename() finds file by partial match")
observed = getObjectFilename(tempdir(), "AAA_BBB.tmp")
checkEquals(observed, expected, "getObjectFilename() finds file by complete match")
observed = getObjectFilename(tempdir(), "A+_B+.tmp")
checkEquals(observed, expected, "getObjectFilename() finds file by regexp")
observed = getObjectFilename(tempdir(), "A+_B+.X?tmp")
checkEquals(observed, expected, "getObjectFilename() finds file by regexp")
unlink(expected)
}
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