[Bioperl-l] SeqFeature scores

Hilmar Lapp hlapp at gmx.net
Thu Oct 16 18:12:13 EDT 2008


On Oct 14, 2008, at 1:28 PM, Chris Fields wrote:

> Personally I'm not sure how we'd store score data in BioSQL.  Is  
> 'score' within the schema?  I suppose we could add it as a specific  
> tag value but that seems potentially hackish and prone to naming  
> conflicts.

Well, yes there might be naming conflicts, if someone wanted to add a  
tag to a seqfeature called 'score', for example.

But would there be cases where it would make sense to have value  
stored in the feature's $feat->score() method *and* a (semantically)  
different one as the 'score' tag's value? Quite frankly I'd be hard- 
pressed to come up with a scenario where that might make sense.

So as far as I am concerned I wouldn't actually have a problem with  
changing the implementation of score() to store/pull the value to/from  
the tag/value hash. In fact, that's what B::SF::Similarity does for  
the attributes it adds methods for (such as bits, significance, etc).

Thoughts? I'm copying this to the Bioperl list as really it is a  
BioPerl/Bioperl-db issue.

	-hilmar

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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