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

Matthew Vaughn vaughn at cshl.edu
Fri Dec 15 13:05:47 EST 2006


Yes, I will. I am working on it today. It's a little more complicated
to fix this than I expected because SeqFeature::Annotation->type()
returns a Bio::AnnotationI rather than a simple scalar like it used
to.

On 12/15/06, Chris Fields <cjfields at uiuc.edu> wrote:
> 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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