[BioRuby] hmmer3

[Ben Woodcroft]

Ah cool, thanks ngoto.

Thanks for writing this Christian. I believe I've extracted the hmmer3
stuff into a new biogem. I've added you as an author on this Christian -
hope that's ok with you?
https://github.com/wwood/bioruby-hmmer3_report

I've not released it to rubygems yet - I wanted to clear up namespace
issues first. What do you suggest Naohisa? BIo::HMMER::HMMER3::Report ?

On looking at the code it seems it only handles tabular format data, which
is rather unfortunate for me, as I need the actual alignment. Looks like
I'll have to roll my sleeves up after all, unless there is yet more code
out there that parses the regular textual format?

I'm not sure about your feelings on this Christian, but how do you feel
about putting the rdf stuff in another biogem? If the aim is to get this
gem merged into the bioruby core code (and I hope it is since when people
say hmmer nowadays they likely mean v3, not v2), maybe the rdf stuff is a
bit tangential?

I also noticed that in the tests Christian referred to BioRubyTestDataPath
which isn't recognised in the biogem. Is there a recommended way to do this
in a biogem? Perhaps we should mirror what bioruby itself does to make the
code more portable.

Thanks everyone for the openness and responsiveness.
ben

On 16 May 2012 21:48, Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:

> Hi Ben,
>
> HMMER3 result parser is written by Christian.
> https://github.com/cmzmasek/bioruby
>
> I guess it may be enough quality, except RDF/XML support
> which is experimental.
>
> I'd like to discuss that the class name Bio::Hmmer3Report
> is suitable. For HMMER2, Bio::HMMER::Report.
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> On Wed, 16 May 2012 21:09:24 +1000
> Ben Woodcroft <donttrustben at gmail.com> wrote:
>
> > Hi guys,
> >
> > I noticed today that there isn't HMMER3 support in bioruby - particularly
> > I'm interested in a parser for hmmsearch outputs as I want to iterate
> over
> > aligned positions.
> >
> > I noticed that there is mention of this in the 1.4.1 release notes, that
> > hmmer3 will be supported in 1.5, although I'm not sure what exactly this
> > means.
> > http://news.open-bio.org/news/2010/10/bioruby-1-4-1-released/
> >
> > Can I ask what the state of this merge is please? Is there code somewhere
> > just waiting to be merged? Can it be quickly spun out into a biogem in
> the
> > meantime?
> >
> > Thanks,
> > ben
> >
> > --
> > Ben Woodcroft
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
>


-- 
--
Ben Woodcroft
http://ecogenomic.org/users/ben-woodcroft <http://www.ecogenomic.org/>