[Bioperl-l] GAME XML format - who's maintaining it?

Chris Fields cjfields at uiuc.edu
Tue Aug 29 15:46:31 EDT 2006


I added a bit to the wiki for deprecating these and recommend using Apollo
instead.  I think there is something in the Apollo docs for conversion (I
remember seeing it somewhere...)

Chris

> -----Original Message-----
> From: Scott Cain [mailto:cain at cshl.edu]
> Sent: Tuesday, August 29, 2006 2:08 PM
> To: Chris Fields
> Cc: 'Sheldon McKay'; 'bioperl-l'; 'Sendu Bala'
> Subject: Re: [Bioperl-l] GAME XML format - who's maintaining it?
> 
> In fact, Apollo also has a command line interface, so it could probably
> be used in a script via system calls to convert between chado xml and
> game xml.  Of course, I've never tried to do that, but it should be
> possible.
> 
> Scott
> 
> 
> On Tue, 2006-08-29 at 13:50 -0500, Chris Fields wrote:
> > Sheldon,
> >
> > What we'll do mark it for deprecation in the next developer release
> unless
> > someone steps up and decides to take care of it.  I noticed the last
> FlyBase
> > release only had Chado XML and no GAME XML, so I guess everyone's
> switching
> > to that.  I'll cc this to Sendu to let him know.
> >
> > I suppose if anyone wants GAME format conversion we should point them to
> > Apollo.  We could probably state that in the deprecation statements.
> >
> > Chris
> >
> > > -----Original Message-----
> > > From: Sheldon McKay [mailto:mckays at cshl.edu]
> > > Sent: Tuesday, August 29, 2006 1:33 PM
> > > To: Chris Fields
> > > Cc: 'bioperl-l'
> > > Subject: Re: [Bioperl-l] GAME XML format - who's maintaining it?
> > >
> > > Hi,
> > >
> > > I rewrote the SeqIO GAME XML modules a couple of years ago but I have
> > > not had much time to maintain them since then.  There does not seem
> > > to be a huge demand for GAME XML support in bioperl and Apollo now
> > > reads and writes chado XML.  Unless someone really wants to keep
> > > these modules around and would be willing to maintain them, I would
> > > vote for deprecation.
> > >
> > > Sheldon
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory



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