[Bioperl-l] Bio::*Taxonomy* changes (Chris Fields)

[Gabriel Valiente]

>> use Bio::DB::Taxonomy;
>
> <SNIPPED OUT GOOD CODE FOR BREVITY>
>
>> I've also written a method to merge the full lineages of a set of
>> Bio::Taxonomy::Node object into a Bio::Tree::Tree object. I'd be glad
>> to contribute it as well, but I'm not sure where it would fit.
>
> Ah, that would be great (I had mentioned something along these  
> lines to do
> with BLAST reports).  But does this actually use Bio::Taxonomy  
> directly?
> Taxonomy::Node does not inherit methods from Bio::Taxonomy AFAIK.  So,
> anything that Sendu does may not dramatically impact your code.   
> Sendu?

It is a general algorithm I devised that takes a set of paths and  
builds up a tree. The input paths are full lineages coming from  
Bio::DB::Taxonomy, the output tree is a Bio::Tree::Tree. This is why  
I said I don't know exactly where it would belong, it looks to me  
more like a standalone script than a Bio::Taxonomy or Bio::Tree method.

Gabriel

> You might need to address some of this to Sendu.  Big changes are  
> afoot for
> Bio::Taxonomy and Bio::Taxonomy::Node.  He's heading that up.
>
> Chris
>
>> ...
>> Thanks a lot. Let me check it and get back to the discussion later  
>> on.
>>
>> Gabriel
>>
>>> Chris
>>>
> ...