[Bioperl-l] *major* error in genbank parser or am i just insane?

[Ewan Birney]

On Thu, 8 Aug 2002, Lincoln Stein wrote:

> Hilmar Sez:
> >  feature) are /not/ the same. You can't collapse this all into one 
> 
> I've been trying to stay out of this, but Hilmar's last comment is driving me 
> nuts.  How do these two statements come to be semantically different?
> 
> 	complement(join(2691..4571,4918..5163))
> 	join(complement(4918..5163),complement(2691..4571))
> 
> They both produce the same DNA sequence in the same orientation.  If GenBank 
> chooses to represent numeric 0 as +0 sometimes and as -0 others, are we 
> morally obligated to maintain the distinction in the data model and round 
> trip it?

I agree with you lincoln, although there is an argument for being able to
round trip it, I think semantic sanity is a good thing.


I vote we go for one representation (strand only on simple features) which
means we are in sync with biosql and it means we will have to take the hit
about not being able to provide a diff-able round-trip...





> 
> Lincoln
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
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