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

[Ewan Birney]

On Thu, 8 Aug 2002, Hilmar Lapp wrote:

> I'm sorry if I was driving anyone nuts. I had about 2 minutes left before the wireless was cut and was concerned about something getting missed and thought this was the bigger risk than me getting flamed for being thoughtless...
> 
> Reconsidering the whole thing, sure, both representations yield exactly the same DNA sequence, and round-tripping is the only issue. I'm happy to dismiss being able to round-trip to the linebreak, semantic sanity is indeed much preferable. Elia, are you OK with this?
> 
> So, as for split locations on the complementary strand, where does
> strand -1 go? Right now the parent is -1 whereas the sublocs are +1.
> This does not map 1:1 to biosql because seqfeatures (the 'parent')
> don't have a strand, and the parent's -1 appears to get lost presently
> when stored in biosql, at least given my copy of the code (older
> versions may not have this problem). Hence, shall we switch to parent
> as strand-less (0) and sublocs on strand -1?

Yup --- sublocs (simples) have strands, parents do not. This is the route
to sanity...


> 
> If I'm again missing something I'm happy to take more flames ...
> 


;) Well... at least everyone is mind sync'd now. Chris - I suspect this is
the solution you wanted...