[Bioperl-l] Bio::Species validate_species_name

Hilmar Lapp hlapp at gmx.net
Mon Sep 19 12:25:37 EDT 2005

If you set the classification array and pass a second argument that 
eval's to true validation is turned off. See 
Bio::Species::classification. This is what the SeqIO parsers do (or 
should do).


On Sep 19, 2005, at 6:56 AM, Stefan Kirov wrote:

> NCBI and Bio::Species have very different views on what is the format 
> of a species field. Is it possible to relax a bit the species regular 
> expression? For example, 'Rhizophidium sp. 136' is a valid NCBI 
> species name, but this is not the case in bioperl (species name in 
> this case is starting with a number). There are other collisions as 
> well, such as special characters found in the species name: ()'/
> Any thoughts?
> Stefan
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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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