tests/countNucleotides.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")
if (fullTest) {

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

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


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

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

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Alignment
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
bams <- doBowtie2(fqs, reference=fa, verbose=-20)
print(bams)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Count nucleotides (single file)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
bam <- bams[[1]]
print(bam)

chrs <- getTargetNames(bam)

## A single chromosomes
loci <- data.frame(chromosome=chrs[1L], pos=1:100)
counts <- countNucleotides(bam, loci=loci, verbose=-10)
print(cbind(loci, counts))

## All chromosomes
loci <- data.frame(chromosome=chrs, pos=1:100)
counts <- countNucleotides(bam, loci=loci, verbose=-10)
print(cbind(loci, counts))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Count and add nucleotides across multiple files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
print(bams)

chrs <- getTargetNames(bams[[1]])
loci <- data.frame(chromosome=chrs[1L], pos=1:100)
counts <- countNucleotides(bams, loci=loci, verbose=-10)
print(cbind(loci, counts))

} # if (fullTest)


############################################################################
# HISTORY:
# 2014-09-28
# o Added test for countNucleotides() on sets.
# 2014-06-15
# o Created.
############################################################################