[BioRuby] hmmer3

[Ben Woodcroft]

Thanks for the feedback dudes. I'm happy to spin it out myself, only I
don't know where the code is.

I don't personally need a wrapper, but I've got 40G of hmmsearch result
files to parse.

Relatedly I've written a gem that parses HMM model files - I'll release
that after a little more testing, hopefully tomorrow.

On 16 May 2012 21:27, Raoul Bonnal <bonnal at ingm.org> wrote:

> If you need to wrap the binary please have a look at our wrapper. I
> wondering is this wrapper could be useful to other gems, I could create a
> separated gem just for it. Let me know. Docs about the wrapper is in the
> readme.
>
> https://github.com/helios/bioruby-ngs/blob/master/lib/wrapper.rb
> https://github.com/helios/bioruby-ngs/blob/master/README.rdoc#wrapper
>
>
> On 16/05/12 13.09, "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
>
>
>