[BioRuby] hmmer3

[Pjotr Prins]

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/