[BioRuby] hmmer3
Pjotr Prins
pjotr.public14 at thebird.nl
Fri May 18 05:21:23 UTC 2012
OK, I'll take the orphaned RDF code.
On Fri, May 18, 2012 at 02:59:44PM +1000, Ben Woodcroft wrote:
> On 16 May 2012 23:46, Pjotr Prins <[1]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:
> [2]https://github.com/wwood/bioruby-hmmer3_report/commit/3795ce3a124011
> cb600e78e6ef10603187c99d20
> 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/[3]biogems.info.
> Thanks,
> ben
>
> References
>
> 1. mailto:pjotr.public14 at thebird.nl
> 2. https://github.com/wwood/bioruby-hmmer3_report/commit/3795ce3a124011cb600e78e6ef10603187c99d20
> 3. http://biogems.info/
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