[Bioperl-l] Phyloxml SeqI without actual sequence

Jason Stajich jason at bioperl.org
Tue Jul 29 12:51:07 EDT 2008


So why would you create the sequence in the first place when it is  
empty? Shouldn't you just not create a sequence if there isn't one?  
Can you provide sample data so we understand better - maybe there is  
sequence name but no data?  Maybe we can specify an option to not  
warn when creating a sequence if a specific flag is provided to the  
Seq initialization routine.

-jason

On Jul 29, 2008, at 9:13 AM, Han, Mira wrote:

>
> Another phyloxml parsing question.
> We have <Sequence> tags that sometimes have actual molecular  
> sequences and
> sometimes don't.
> I decided to create a SeqI object and link it to AnnotatableNode.
> But when it doesn't have actual sequence
> It gives warning that the sequence is empty.
> I don't think it's a big problem,
> And I'd prefer having consistency than having two different  
> solutions for
> the same tag.
> But I'd like to hear people's opinion on this as well.
> Thank you
>
> Mira Han
>
>
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