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Gmane
From: Chris Mungall <cjmungall <at> lbl.gov>
Subject: Re: Bio::FeatureIO::faldo
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Tuesday 16th July 2013 21:23:45 UTC (over 3 years ago)
Thanks Chris!


On Tue, Jul 16, 2013 at 11:05 AM, Fields, Christopher J <
[email protected]> wrote:

> Chris (m),
>
> It's merged in; you can technically make commits directly or to a branch
> as you are in the list of developers, so no forking is necessary.
>
> Re: FeatureIO, it will be a separate release series from bioperl core
> (it's not on CPAN on it's own as of yet, though it likely will be in the
> next month or two).
>
> chris (f)
>
> On Jul 11, 2013, at 4:27 PM, Chris Mungall  wrote:
>
> > Hi all,
> >
> > I wrote a bioperl module for generating RDF/turtle for features using
> the FALDO model [1]
> >
> > I think this is the first time I've contributed code to bioperl since
> the brave new world of github - I suppose as I am a developer I could
have
> added it straight in but I forked and made a pull request
> >
> >       https://github.com/bioperl/Bio-FeatureIO/pull/2
> >
> > Is this the correct protocol?
> >
> > There's a bit more work to do - mapping all the various GFF attributes
> to the desired properties is something that requires broader discussion
in
> the GFF3/FALDO communities.
> >
> > The sensible thing to do would be to compare the output with Rob
> Hoehndorf's Groovy GFF3 to FALDO converter - I confess I haven't done
this
> yet.
> >
> > For the FALDO folks, this allows a wider range of formats to be
> converted to FALDO, and makes it easier to use FALDO from within existing
> bioperl based architectures.
> >
> > Cheers
> > Chris
> >
> > [1] https://github.com/JervenBolleman/FALDO
> > _______________________________________________
> > Bioperl-l mailing list
> > [email protected]
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
 
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