[ensembl-dev] Bio::Species doesn't like scientific names containing brackets

Chris Fields cjfields at illinois.edu
Wed Jun 29 14:54:50 BST 2011


Just want to point out this problem has been generally solved in the latest BioPerl, in that we deprecated Bio::Species due to fussiness with parsing this data (it's just not possible to cover every edge case).  It's possible this has been fixed though.

chris

On Jun 29, 2011, at 6:02 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.
> 
> Does anyone know what should be happening here? Are brackets allowed, and if so, how should Bio::Species be dealing with them?
> 
> The runtime error would be easy to trap by escaping the text in the regex, but I suspect that really the problem is that species/subspecies shouldn't contain brackets in the first place (?)
> 
> Cheers,
> Nick
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