[Bioperl-l] Bio::Species validate_species_name

Stefan Kirov skirov at utk.edu
Tue Sep 20 13:06:21 EDT 2005

Before I modify entrezgene to override the classification verification I 
have a question - what's the reason to do that? What about the danger of 
inconsistencies down the road? One can imagine a situation, where the 
parser having passed a bad classification creates invalid binomial name, 
which then breaks the user's code (for example database queries, file 
structure, etc.).

Hilmar Lapp wrote:

> 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).
>     -hilmar
> 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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