[Biopython] getting the parent of a Clade

[Michael Thon]

On Oct 31, 2010, at 8:23 PM, Eric Talevich wrote:

> 
> 
> On Sun, Oct 31, 2010 at 1:57 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Sun, Oct 31, 2010 at 12:03 PM, Michael Thon <mike.thon at gmail.com> wrote:
> I have a Clade object and I need to access its parent clade.  I thought that clade.root should do this but this seems to contain a reference to itself:
> 
> (Pdb) main_clade == main_clade.root
> True
> 
> Is there some other way?
> Thanks
> Mike
> 
> 
> Hi Mike,
> 
> You can do this, assuming you have the original tree object (call it "tree"):
> 
> parent = tree.get_path(main_clade)[-2]
> 
> This is an O(n) operation on the tree, so if you need to do it repeatedly on a large tree, it's faster to call tree.get_path(clade) once outside the loop and then reuse the resulting list.
> 
> Is the operation you're doing here part of something you'd like to see implemented as a tree method?
> 
> 
Maybe - it seems to me that if I can access children of a clade from the clade, then I should also be able to go the other way and access the parent.  I don't know how often people would need this functionality though.

Does a Clade contain a reference to its tree? I have a recursive function that does some crunching on a Clade and then recursively processes the child clades.  I could pass in  the tree object as well, but I figure that a Clade must know about its tree so there should be some way to access it.

Thanks
Mike

> I added a cookbook entry on the Biopython wiki for this problem:
> http://biopython.org/wiki/Phylo_cookbook#Get_the_parent_of_a_clade
> 
> Cheers,
> Eric