[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)

[Hilmar Lapp]

On Aug 23, 2009, at 1:17 PM, Anand C. Patel wrote:

> [...]
> Code snippet:
> my $species = $seq->species;
> print "common name = ",$species->common_name, "\n";
> print "scientific name = ",$species->scientific_name, "\n";
> print "species = ",$species->species, "\n";
> print "genus = ",$species->genus, "\n";
> print "sub_species = ",$species->sub_species, "\n";
> print "binomial = ",$species->binomial, "\n";
> print "ncbi_taxid = ",$species->ncbi_taxid, "\n";
>
> Output:
> common name =
> scientific name = musculus
> species = musculus
> genus = Mus
> sub_species =
> binomial = Mus musculus
> ncbi_taxid = 10090

This points to a problem in Bio::Species::scientific_name(), given  
that binomial() is correct. Could you file this as a bug report?

> The common name is missing, despite having loaded it from NCBI  
> taxonomy using the provided script.
> It is ONLY present as this "genbank common name".
> [...]
> I could go through and replace all of the instances of "genbank  
> common name" with "common name" and see if this fixes it.
I think we need to first discuss how we want to treat the 'common  
name' versus 'genbank common name' classes in BioPerl.

So question for everyone: do we need to have both available (in which  
case we need to add an accessor in Bio::Species), or only 'common  
name', or should 'genbank common name' override 'common name' if both  
are present and have different values.

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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