test_writeXStringSet <- function()
{
tmpdir <- tempdir()
tmpfilefa <- file.path(tmpdir,"whee.fa")
tmpfilefq <- file.path(tmpdir,"whee.fq")
x1 <- DNAStringSet(c("TTGA", "CTCN"))
q1 <- PhredQuality(c("*+,-", "6789"))
qdna1 <- QualityScaledDNAStringSet(x1, q1)
names_dna <- c("A", "B")
names(qdna1) <- names_dna
writeXStringSet(x1, format="fasta", file=tmpfilefa)
dna1 <- readDNAStringSet(tmpfilefa, format="fasta")
checkTrue(is.null(mcols(dna1)))
checkTrue(all(names(dna1) == c("","")))
names(x1) <- names_dna
writeXStringSet(x1, format="fastq", file=tmpfilefq)
qdna2 <- readQualityScaledDNAStringSet(tmpfilefq)
checkTrue(!all(quality(qdna2) == quality(qdna1)))
checkTrue(all(all(as(quality(qdna2),"IntegerList") == 26L)))
writeXStringSet(x1, format="fastq", file=tmpfilefq, qualities = q1)
qdna2 <- readQualityScaledDNAStringSet(tmpfilefq)
checkTrue(all(quality(qdna2) == quality(qdna1)))
writeXStringSet(qdna1, format="fastq", file=tmpfilefq)
qdna2 <- readQualityScaledDNAStringSet(tmpfilefq)
checkTrue(all(names(qdna2) == names_dna))
checkTrue(all(quality(qdna2) == quality(qdna1)))
qdna2 <- readDNAStringSet(tmpfilefq, format="fastq")
checkTrue(is.null(mcols(qdna2)))
qdna2 <- readDNAStringSet(tmpfilefq, format="fastq", with.qualities = TRUE)
checkTrue(all(mcols(qdna2)$qualities == quality(qdna1)))
unlink(tmpfilefa)
unlink(tmpfilefq)
}
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