[Bioperl-l] Bio::SeqFeature::Annotated API change

[Chris Fields]

On Oct 12, 2007, at 10:06 AM, Sendu Bala wrote:
...

>
> I still don't really understand what the deal is with all these  
> modules,
> so I'll leave it your hands to make further recommendations and  
> take action.
>
> From my limited understanding what you said seems reasonable,  
> except for
> excluding FeatureIO completely. At least, I'd really like to see it in
> 1.6; it would be a shame to miss it just because of Annotated. Worst
> case, isn't Generic 'good enough' as a replacement?

It probably could work, but type checking, ontology_term(), and SF  
data validation wouldn't be implemented immediately as it would  
require additional code.  I'll try looking into it this weekend to  
see what needs to be done and work from there.

>> The GMOD meeting is a few weeks away, where I assume some things will
>> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
>> saving; maybe retooling it would be in our best interests, but it
>> needs a decent roadmap to move forward.
>
> Agreed. I guess we'll wait for the results of that meeting? Is  
> anyone going planning to discuss this issue?

Jason is going to be there and intends to bring it up as it affects  
GBrowse/GMOD/Chado.

chris