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
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