tests/TopHat2Alignment,PE,future.R

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

library("aroma.seq")

fullTest <- (Sys.getenv("_R_CHECK_FULL_") != "")
fullTest <- fullTest && isCapableOf(aroma.seq, "bowtie2")
fullTest <- fullTest && isCapableOf(aroma.seq, "samtools")
fullTest <- fullTest && isCapableOf(aroma.seq, "tophat2")
if (fullTest) {

library("future")
strategies <- c("lazy", "eager")
if (future::supportsMulticore()) strategies <- c(strategies, "multicore")
if (require(pkg <- "future.BatchJobs", character.only=TRUE)) {
  strategies <- c(strategies, "batchjobs_local")
}

dataSet <- "YeastTest"
organism <- "Saccharomyces_cerevisiae"

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


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Annotation data
fa <- FastaReferenceSet$byOrganism(organism)
print(fa)

# FASTQ data
fqs <- FastqDataSet$byName(dataSet, organism=organism, paired=TRUE)
print(fqs)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# TopHat2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
is <- buildBowtie2IndexSet(fa, verbose=TRUE)  # is = 'index set'
print(is)

for (strategy in strategies) {
  plan(strategy)
  print(plan())

  # Align input reads using TopHat
  ta <- TopHat2Alignment(dataSet=fqs, indexSet=is, tags=c("*", strategy))
  process(ta, verbose=-100)
  
  bams <- getOutputDataSet(ta)
  print(bams)
  
  # Sanity checks
  stopifnot(length(bams) == length(fqs))
}

} # if (fullTest)