[Bioperl-l] bond() operator

[Hilmar Lapp]

On Monday, March 3, 2003, at 08:20  AM, Ewan Birney wrote:

> Well... is this a bug?
>
>
> http://www.ebi.ac.uk/embl/Documentation/FT_definitions/ 
> feature_table.html#operators
>
> bond is not in there.
>

Right. That's why I sent a grumbling email when this first came up  
whether Genbank wants to repeat the same mistake (mistake IMHO anyways)  
it made a while ago with annotating polymorphisms, namely to fold  
annotation into the location string.

With polymorphisms, they used the dreaded replace('A', 100) syntax.  
Meanwhile they corrected this and it's now a feature with key  
'variation' and standard location syntax.

Having annotation and location folded into the same string really  
creates a whole mess in bioperl with regard to parsing this out in a  
structured manner, and even worse, round-tripping. So, quite honestly,  
I do hope that NCBI backs off of that, as they did for replace(). But  
maybe I'm missing something.

	-hilmar

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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