[BioC] XStringViews with strand?

[Cei Abreu-Goodger]

Hi all,

I'm trying to read in a fasta sequence, extract the "gene sequences" and 
write these out to a fasta file. I can read the sequences with 
read.DNAStringSet(), obtain an XStringViews object with Views(), but I'm 
having trouble knowing how to obtain the reverse complement sequence for 
the genes on the "-" strand. I can get them with a reverseComplement()
of the XStringViews object, but I can't overwrite the elements of this 
object. So my solution involves dealing separately with all the genes on 
the "+" strand and those on the "-" strand. Is there an easier way?

An example:

file <- system.file("extdata", "someORF.fa", package="Biostrings")
x <- read.DNAStringSet(file, "fasta")[[1]]

names   <- c("a","b","c")
starts  <- c(10,384,947)
ends    <- starts+20
strands <- c("+","-","+")

myViews <- Views(x, start=starts, end=ends)
names(myViews) <- names

revViews <- reverseComplement(myViews[strands=="-"])
posViews <- myViews[strands=="+"]


Many thanks,

Cei

sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
[1] Biostrings_2.12.1 IRanges_1.2.2     Biobase_2.4.1