Hi Herve, Thanks for the info. I'll check out the devel version soon, and I guess I'll be doing something like what you suggest: myDNAStringSet <- as(myViews, "DNAStringSet") myDNAStringSet[strands == "-"] <- reverseComplement(myDNAStringSet[strands == "-"]) Cheers, Cei Hervé Pagès wrote: > Hi Cei, > > Cei Abreu-Goodger wrote: >> 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=="+"] > > Yes it has to be done separately. The content of a view cannot be modified > because that would mean modifying the underlying subject so you would end > up with a subject that is a mix of + and - strand. And what should be done > when 2 views overlap, 1 being associated with a gene on the + strand and > the other one with a gene on the - strand? > > In the near future we will support replacement of the elements of a > DNAStringSet > object through "[<-" and "[[<-". Then it will be possible to > reverseComplement > some of its elements with something like this: > > x[strands == "-"] <- reverseComplement(x[strands == "-"]) > > But that will be for XStringSet only, not for XStringViews. > > These developments will take place in the devel version of Biostrings in > the > next few weeks. > > Cheers, > H. > > >> >> >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.