tests/FastqDataSet,SE.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

library("aroma.seq")

fullTest <- (Sys.getenv("_R_CHECK_FULL_") != "")

# Setup (writable) local data directory structure
setupExampleData()


dataSet <- "TopHat-example"
organism <- "Lambda_phage"

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# Setup FASTA reference file
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fa <- FastaReferenceFile$byOrganism(organism)
print(fa)

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# Setup FASTQ set
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fqs <- FastqDataSet$byName(dataSet, organism=organism, paired=FALSE)
print(fqs)
for (ii in seq_along(fqs)) print(fqs[[ii]])


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# Gzip data set
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dataSetZ <- sprintf("%s,gz", dataSet);
pathZ <- file.path("fastqData", dataSetZ, organism)
for (ii in seq_along(fqs)) {
  fq <- fqs[[ii]]
  pathnameZ <- file.path(pathZ, sprintf("%s.gz", getFilename(fq)))
  gzip(getPathname(fq), pathnameZ, skip=TRUE, remove=FALSE)
}


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# Setup gzip'ed FASTQ set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fqsZ <- FastqDataSet$byName(dataSet, tags="gz", organism=organism, paired=FALSE)
print(fqsZ)
for (ii in seq_along(fqsZ)) print(fqsZ[[ii]])


# Assert that file extensions are properly dropped
stopifnot(all(getFullNames(fqsZ) == getFullNames(fqs)))