Hi Herve,

What would be a clean way for rtracklayer to extract the (optional) FASTA
data embedded in a GFF3 file and parse it as an XStringSet? Is there a
low-level way to pass in-memory data to the parser in Biostrings?

In terms of the API, import,GFFFile could return a GRanges with the
DNAStringSet in the metadata(). Or there could be a method for
readDNAStringSet on GFF3File that returns the DNAStringSet directly.

It turns out this functionality is useful when working with microbial
genomes, where information tends to be passed around as Genbank files. For
right now the easiest path seems to be to convert Genbank to GFF, but a
Genbank parser in Bioc could be an eventual goal. It's a very complex file
format.

Michael

	[[alternative HTML version deleted]]

