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

[Lincoln Stein]

Here's my 2c:

If the genbank entry has CDS features but no exons, or an mRNA join operator 
which is out of sync with the CDS join, then in my opinion the quality of the 
annotation is so questionable that BioSQL should throw up its hands and seek 
human assistance in interpretation.  Asking the import software to read the 
minds of the submitters is beyond what can be reasonably expected, and only 
ends up propagating errors.

Lincoln

On Friday 09 August 2002 04:49 am, 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...
>
> Regards,
> Brian
>
>
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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