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

Scott Cain cain at cshl.edu
Tue Aug 29 15:08:05 EDT 2006


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
> 
> 
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-- 
------------------------------------------------------------------------
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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