[Bioperl-l] Bio::SeqFeature::Annotated and mandatory type checking

Chris Fields cjfields at uiuc.edu
Fri Dec 15 12:49:45 EST 2006


On Dec 14, 2006, at 11:01 PM, Scott Cain wrote:

> As much as I would like to take credit for this :-)  Allen Day  
> wrote the
> original code, and then Chris Fields tried to fix it so that it  
> actually
> worked :-)  I think it would be a good idea to have a validate_terms
> option like Bio::FeatureIO::gff.
>
> Scott

I did ?!?  I committed a bug fix a while back:

Revision 1.34 / (view) - annotate - [select for diffs] ,
Sun Jul 23 18:00:50 2006 UTC (4 months, 3 weeks ago) by cjfields
Branch: MAIN
CVS Tags: branch-experimental
Branch point for: branch-1-5-2
Changes since 1.33: +155 -33 lines
Diff to previous 1.33

Bug 2026; Robert's enhancements

To tell the truth I don't know if this is where the mandatory checks  
were added in; I'm not too familiar with SeqFeature::Annotation yet.

I agree with Scott (and Matthew) that SOFA checks should be  
optional.  Matthew, can you write up a patch and maybe some tests?

chris





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