[BioRuby] hmmer3

[Ben Woodcroft]

On 16 May 2012 23:46, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> On Wed, May 16, 2012 at 11:28:01PM +1000, Ben Woodcroft wrote:
> > maybe the rdf stuff is a
> > bit tangential?
>
> I think it should be decoupled. RDF, in general, is a (searchable)
> result-based (post-parser) format. Maybe we should coin that
> definition somewhere :). I created bio-rdf biogem as a 'sink' for RDF
> into triple stores. Sounds that bio-rdf is the right place for that
> translation code to me :).  Feel free to push it in.
>

Thanks. I've removed the rdf related code all in one commit:
https://github.com/wwood/bioruby-hmmer3_report/commit/3795ce3a124011cb600e78e6ef10603187c99d20

However, I don't feel like I should be adding this to a different
repository because I don't feel like I understand the technology enough,
and therefore am not really inclined to maintain it. All of the relevant
code should be in that commit, so should be quite simple to add in yourself
if you are inclined (though I couldn't find any unit tests). Only, I've
changed the namespace of it to Bio::HMMER::HMMER3::Report from
Bio::Hmmer3report as Naohisa suggested. I've also now pushed the new biogem
to rubygems/biogems.info.

Thanks,
ben