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

[Ewan Birney]

On Fri, 9 Aug 2002, Brian King wrote:

> 
>  
> > This is very hard to do because you have to handle:
> > 
> > 
> >    (a) CDS with no Exons 
> > 
> > and, my particular favourite
> > 
> >    (b) a mRNA join operator which is out of sync
> > with the CDS join
> > operator (!)
> 
> For (a) I'd put generic sub-features in the CDS to
> hold the places of the presumed exons, and for (b) use
> generic sub-features for the CDS and the mRNA joins
> and just let them be out of sync.  I surrender on
> remote joins!  I'd keep the location string in
> documentation in the data, but not try to interpret
> it.  Ideally the parser would download the remote
> record, but...

This just get more and more complex as more and more bizarre cases come
out of the woodwork...


This is a good thing. The question is who will do it. Are you
volunteering?




>  
> Regards,
> Brian
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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