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

Sheldon McKay mckays at cshl.edu
Tue Aug 29 14:32:57 EDT 2006


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


On Aug 28, 2006, at 5:46 PM, Chris Fields wrote:

> What is the current status for support of this sequence format for  
> Bioperl?
> The SeqIO modules don't seem to be maintained, and I don't know the  
> current
> status of the GAME sequence format.  Should these be deprecated?
>
> I noticed several problems with GAME format parsing while looking  
> at this
> bug:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=1954
>
> I would rather not spend time on a SeqIO module where a majority of  
> the XML
> tags seem to be ignored, the parsing is broken, the write_seq() is
> incomplete, etc.
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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