[Bioperl-l] undef SeqFeature tag values

Chris Fields cjfields at uiuc.edu
Fri Aug 24 18:36:46 EDT 2007


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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