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

[Hilmar Lapp]

On Aug 22, 2009, at 9:13 PM, Anand C. Patel wrote:

> Turns out that using the default namespace bioperl doesn't change  
> anything.

No it shouldn't, so long as you are consistent about it. (And if  
you're not, all that should happen is that you don't find your  
sequences any more.)

>
> Common name -- still "genbank common name" in name_class in the  
> taxon_name table for "house mouse", which I think the module is  
> looking for as "common name".

If you are loading the NCBI taxonomy first, this is coming from NCBI,  
not one of the scripts or BioPerl, and hence we have no control over  
it. Are you saying that there is no designated name of class 'common  
name' for Mus musculus in the NCBI taxonomy dump?

Also, the common name being present or not should have no bearing on  
the lineage array, where the actual problem is, so I don't understand  
right now how this would be connected to the problem you are seeing.

>
> It's not behaving differently despite reloading the sequences.
>
> I've created a horrible munge that fixes it for cosmetic purposes:
> my $species = $seq->species;
> my $justspecies = $species->scientific_name();
> my $binspecies = $species->binomial();
>
> my $gbstring2 = $gbstring;
>
> $gbstring2 =~ s/$binspecies/$justspecies/g;
> $gbstring2 =~ s/$justspecies/$binspecies/g;

I don't understand what you are trying to achieve here - it seems like  
you are making a substitution and then reverting it? Also, $species- 
 >scientific_name() and $species->binomial() should be identical for  
Mus musculus - are you finding different values being returned?

So in essence, I wouldn't expect your above code snippet to have any  
effect, for both of these reasons. How do you find $gbstring2 to be  
different from $gbstring at the end of this block of code?

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