[BioRuby] GFF3

[Naohisa GOTO]

On Mon, 16 Aug 2010 14:05:30 +0200
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> The GFF3 module parses GFF3 files and stores them in memory. We could
> do something with that data. Most people will want to fetch mRNA and
> CDS's. BioPerl has some similar facility.
> 
> How about adding a module GFF3::Sequence with methods that fetch the
> mRNA (splicing) variants and CDS's that belong to an ID? Or do you
> think an implementation would be ambiguous?

Currently, the GFF parser in BioRuby is currently based on lines.
To treat  relations in the lines in a GFF3 file will be needed.
A simple implementation would be to store all relations into a
graph (or graphs) and then extracting information.

BTW, for extracting sequence, I prefer GFF3::SequenceCutter or
ExtractSequence rather than GFF3::Sequence.


> Or is that already in there? I must admit I can't find it.

No.


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org