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

[Nick Langridge]

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