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

[Ewan Birney]

On Wed, 7 Aug 2002, Hilmar Lapp wrote:

> I have no idea what the present status on that is, but my reply was 
> generally not about a long-term/high-level/design/it would
> be much better if/ discussion. I basically asked the question what 
> complement(join(1..100,201..300)) exactly means, and whether it has 
> been decided how exactly it shall be translated into strand() 
> attributes of the parent and sub-locations. This hasn't been 
> answered yet ...
> 
> Quoting from the FT definition:
> 
> complement(join(2691..4571,4918..5163))
>                           Joins regions 2691 to 4571 and 4918 to 
> 5163, then 
>                           complements the joined segments (the 
> feature is 
>                           on the strand complementary to the 
> presented strand)
>  
> join(complement(4918..5163),complement(2691..4571))
>                           Complements regions 4918 to 5163 and 2691 
> to 4571, then 
>                           joins the complemented segments (the 
> feature is 
>                           on the strand complementary to the 
> presented strand)
> 
> The case in question is the first example. To translate this 
> properly to Bioperl locations, this means the parent SplitLoc is 
> strand -1, whereas the subs are strand +1. Right?
> 

I consider these two semantically equivalent, and I think bioperl should,
but of course, for round tripping, nicer to represent it I guess...