[Bioperl-l] Species validation

[Hilmar Lapp]

On Tuesday, September 24, 2002, at 12:59 AM, Ewan Birney wrote:

>
>
> At the moment as people have noticed we are blowing up on impossible to
> decipher species. Of course, some of these really are impossible to
> decipher, like the mouse/rat hybrid thing (though it slightly 
> annoys me -
> surely this thing *came* from either mouse or rat!)
>
>
> What I suggest is that we test whether the classification strings make
> sense - if they do, we make a standard species object. If not, we 
> make a
> specific "unknown species" object, classification "unknown", species
> "unknown" but store the original strings somewhere.
>
>
>
> Any other thoughts - throwing exceptions is not good in the middle 
> of EMBL
> parsing and just letting anything go in there is also not good...
>
>

What about a warning?

Setting all slots to 'unknown' is not very helpful if you are going 
to serialize this entry to a database.

	-hilmar

>
>
> What does genbank do for these entries?
>
>
>
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--
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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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