[Bioperl-l] Script taxonomy2tree version 1.4 crashed on 110 species

[Sendu Bala]

Chris Fields wrote:
> 
> On Dec 18, 2006, at 1:15 PM, Sendu Bala wrote:
> 
>> For example, the first 'drop' happens for the 101st species which is
>> 'Leptospira interrogans serovar Copenhageni'. This is a variation
>> (descendant) of species 24: 'Leptospira interrogans'. So when the
>> variation is added it becomes a leaf and 'Leptospira interrogans' is no
>> longer a leaf, so the overall number of leaves does not increase.
>
> Makes sense now.  I personally would consider this a bug since the 
> results are unexpected (so the docs need to be modified in order to 
> clarify).  Some say tomato...
> 
> I suppose this is one of the issues one might run into when using NCBI 
> taxonomy to build trees.

No, the tree produced is perfectly fine. The taxonomy2tree.pl script 
deliberately then does:

# simple paths are contracted by removing degree one nodes
$tree->contract_linear_paths;

Because that is what Gabriel's script originally did.


>> Gabriel, please confirm this isn't a bug, or suggest how you propose to
>> see your taxa when they are not all leaves of the tree.
> 
> Having the nodes appear internally seems semantically correct to me.  Is 
> there any other way?

I suppose if we want to see all the input species output again we have 
to make contract_linear_paths() aware of nodes we want to keep, even 
when they are degree one nodes. Gabriel, is that what you want to see?