[Bioperl-l] Bio::Species bug report - cannot handle scientific names containing brackets

[Chris Fields]

You are more than welcome to file a bug, but we don't really support parsing this data anymore (the reason why Bio::Species is deprecated).  It's just too fraught with problematic edge cases to work in all instances.

chris

On Jun 29, 2011, at 8:44 AM, Nick Langridge wrote:

> Hi,
> 
> I'm having problems with Bio::Species and species that have brackets in thier scientific names, e.g. "Buchnera aphidicola (subsp. Acyrthosiphon pisum, strain 5A)".
> 
> Bio::Species tries to extract the genus, species, and subspecies from the scientific name, but it ends up with mismatched brackets, e.g.
> genus:  "Buchnera"
> species: "aphidicola (subsp."
> subspecies: "Acyrthosiphon pisum, strain 5A)"
> 
> This causes an 'Unmatched ( in regex' runtime error when the module later tries to use the species value directly in a regex (in the binomial sub).
> 
> I'm not sure if this module is maintained (?) as the docs say it is deprecated (unfortunately my circumstances mean I can't avoid it) but if it is and you'd like a more detailed bug report then I can provide one.
> 
> Best regards,
> Nick
> 
> -----------------------------
> Nick Langridge
> Ensembl Genomes Web Developer
> EMBL-EBI
> http://www.ensemblgenomes.org
> 
> 
> 
> 
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