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

[Brian King]

> 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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