[Bioperl-l] Re: [apollo] Game XML parser

[Lincoln Stein]

Hi Sheldon, Nomi, et al.,

Nomi is completely right.  The gbrowse incompatibility problem is secondary to 
the incompatible Bio::SeqIO::game issue, and this is what's bugging Sheldon.  
I've recently gotten the up-to-date GAME/XML DTD from Colin (thanks Colin!) 
and am going to dig into the Game/XML parser ASAP.

I can't guarantee a due date because I'm busy with the gbrowse synteny browser 
(sound familiar, Nomi?) but I think the synteny browser will be "done" early 
this week, which means that I can start work on the GAME/XML issues.

Lincoln


On Saturday 19 April 2003 11:55 pm, Nomi Harris wrote:
> Lincoln and/or Chris,
>
> Is this related to the issue where the version of GAME written by gbrowse
> is not the same as the one that Apollo uses?  Will Sheldon's problem with
> the incompatible Bio::SeqIO::game be solved when the gbrowse issue is
> solved, or is that a separate codebase?
>
> Thanks,
> 	Nomi
>
> On 19 April 2003, smckay at bcgsc.ca wrote:
>  > Hi,
>  >
>  > I am interested in using the apollo annotation editor but I am finding
>  > the reliance on game XML to be somewhat of a barrier.  In my hands, the
>  > apollo (v 1.2.6) Genbank data adpater is not working.  So, in the mean
>  > time, I'd like to parse my saved annotations (in game XML) into a
>  > Bio::SeqIO object so I can save them in whatever format but, alas,
>  > Bio::SeqIO::game is not compatible with the apollo flavor of game.
>  > I am able to use the BDGP/flybase parser (BioModel::AnnotationIO::Game)
>  > to get a BioModel::Annotatedseq object but now I don't know what to do
>  > with it.  Sigh. Can anyone help?
>  >
>  > Thanks,
>  > Sheldon
>  >
>  >
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>  > apollo at mail.fruitfly.org
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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