Thanks Martin This was thought as a feauture request/discussion of biostrings, which is why I posted it here. Thought biostrings io capabilities was behind most other fasts readers on bioconductor...
/Thomas > Den 29/01/2015 kl. 15.45 skrev Martin Morgan <mtmor...@fredhutch.org>: > >> On 01/29/2015 06:41 AM, Thomas Lin Pedersen wrote: >> Hi >> >> I’m querying on whether there are any plans on supporting random access >> reading of fasta files in the sense that it is possible to upfront specify >> the indexes of sequences that should be read in. >> >> I’m working on a package for comparative microbial genomics and it would be >> a huge speed improvement if it was possible to quickly read in 1000’s of >> sequences distributed on as many files. Currently the proper, vectorised >> approach requires all files to be read in at once and then subsetted, but >> this can result in XStringSet’s in the Gb range, just to access some >> sequences. The slow, un-R way would be to loop through each file (or each >> sequence using skip and nrec to only read in relevant sequences). I’m >> preferentially looking for an interface like: >> >> readXStringSet(files, rec) >> >> Where rec is either a vector that would index into the XStringSet as if >> everything from files had been read in, or a list with the same length as >> files, containing the indexes of interest for each file. > > Hi Thomas -- this should really be posted to support.bioconductor.org, but > see Rsamtools::FaFile and rtracklayer::TwoBitFile access through getSeq. > > Martin > >> with best wishes >> >> Thomas >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
