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

[Ewan Birney]

On Wed, 7 Aug 2002, Chris Mungall wrote:

> 
> i would have though the sublocations strand should be -1, as they
> represent exons on the reverse strand. but i don't really understand the
> whole bioperl location+seqfeature semantics/model; when outside the
> bioperl world i just have one class that rolls seqfeature and location
> into one.
> 
> i'm happy to have hilmar revoke my fix and instead go with checking the
> parent location strand rather than the sublocation strand (if someone
> could fix the genbank dumper to print the complement correctly that would
> be great). if we go this route i will fix bioperl-db so that the parent
> location strand goes into the seqfeature_location table. note that this
> will introduce a slight disjunction between biosql abnd bioperl (in biosql
> we absolutely must represent -ve strand exons as
> seqfeature_location.strand = -1). hmm, how does biojava handle this.


I do prefer chris' semantics to having to hold onto the difference between
a parent complement and a child complement - ie, I think we should
implicitly only allow the complement to happen on simple sequence
locations and never splits, and genbank with an outer complement is an
implicit distributive complement and reverse of its components. 


...nasty.... either way we look at it, becuase people will moan about not
round tripping genbank.


If anyone makes a semantic difference between parent vs child complements
I am worried...