Thanks Martin, that's exactly what I was looking for! (missed the showMethods("getSeq"), sorry) On 10/28/12 5:49 PM, Martin Morgan wrote: > On 10/28/2012 11:28 PM, Cei Abreu-Goodger wrote: >> Hello all, >> >> I was wondering if there was a simple way to get the sequences >> corresponding to >> the ranges stored in a GRanges object. If you have the original >> sequences in a >> BSgenome object, you can use 'getSeq'. But what if you just have the >> fasta file, >> imported as a DNAStringSet object? >> >> I want to avoid having to forge a new BSgenome object each time, since >> I'm >> dealing with unfinished assemblies, with thousands of sequences that I >> don't >> want to split into individual fasta files, etc. > > Rsamtools has FaFile and FaFileList to represent (indexed, via indexFa) > fasta files, and a getSeq method that takes an FaFile and a GRanges (or > similar) object. This is built on top of scanFa. See > > library(Rsamtools) > method?"getSeq,FaFile" > > Martin > >> >> Many thanks, >> >> Cei >> > > -- Dr. Cei Abreu-Goodger Profesor Investigador Langebio CINVESTAV Tel: (52) 462 166 3006 cei at langebio.cinvestav.mx -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.