[Bioperl-l] undef SeqFeature tag values

Chris Fields cjfields at uiuc.edu
Sat Aug 25 00:05:58 EDT 2007


Makes sense.  Okay, I'll leave the exception in.  Thanks!

chris

On Aug 24, 2007, at 6:02 PM, Hilmar Lapp wrote:

> You're supposed to call has_tag() first before you can assume that
> you can call get_tag_values() w/o an exception. That was the original
> API.
>
> 	-hilmar
>
> On Aug 24, 2007, at 6:36 PM, Chris Fields wrote:
>
>> One thing I am noticing with the rollback to tag as strings is that
>> tags with an undefined value are not set; I'm assuming when tags were
>> Bio::AnnotationI they were instantiated regardless with an undef
>> value.  When attempting to call an undef tag with get_tag_values() I
>> get:
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: asking for tag value that does not exist signalPeptideLength
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /Users/cjfields/src/featann_rollback/
>> bioperl-live/blib/lib/Bio/Root/Root.pm:357
>> STACK: Bio::SeqFeature::Generic::get_tag_values /Users/cjfields/src/
>> featann_rollback/bioperl-live/blib/lib/Bio/SeqFeature/Generic.pm:499
>> STACK: t/targetp.t:189
>> -----------------------------------------------------------
>>
>> I personally think of this as a feature (why set a tag at all if it
>> is undef?).  However, are there any circumstances where we might want
>> this behavior?  Do we want to simply return w/o a value if a tag name
>> isn't found (i.e. remove the exception)?
>>
>> chris
>>
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>> Bioperl-l at lists.open-bio.org
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>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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