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

[Sendu Bala]

Hilmar Lapp wrote:
> 
> 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?

What code creates the Bio::Species object here? I suspect this code 
isn't aware of changes in Bio::Species since BioPerl 1.5.2.


>> 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.

Bio::Species (via Bio::Taxon) has the common_names() method, for which 
common_name() is an alias that in scalar context returns the first of 
possibly many common names, one of which may be the genbank common name.

See:
http://www.bioperl.org/wiki/Core_1.5.2_new_features#Implementation_changes