agormp / phylotreelib Goto Github PK

Hi,
thanks for the work and the lib. I have a problem with the spr (subtree pruning and regrafting) function, which I would like to use to create randomly different topologies of a strictly bifurcating tree.
If I take as the source node a leaf and not an internal node this leads to internal nodes being non-bifurcating (just one additional internal node between the original internal node and the leaf) and this can lead in newick representation even to unmatching opening and closing parentheses. Is it not possible to prune leaves or is there a workaround how I can remove these introduced non-bifurcating internal nodes?

Also, I find it quite difficult/verbose to define all conditions to filter possible regrafting nodes after I picked (randomly) a pruning node from the tree (which doesn't lead to an Error due to being a (remote - also internal) child of the same node or a parent or root or the other children of the parent node...). Is there maybe a function (planned) which makes this easier and gives potential options to do random spr moves on a tree?

Thanks a lot in advance and again thanks for your work with this library!
Elias

P.S.: I wrote for this some helper functions like a recursive "_get_all_remote_children()" function to get all remote child nodes, not just remote child leaves or an "_is_rotation_variant()" to check for rotation variants of two trees (or is this already solved by comparing the (sorted) newick representations?) - if these are ideas for future additions to the lib and you are interested, I'm happy to share.

Hey again,
I detected a bug in the treedist() function, which returns 0.0 (i.e. no difference) between two trees with different topologies such as these (ete3 normalised robinson-foulds dist for comparison):

import phylotreelib as pt
import ete3
a = pt.Tree.from_string('(A,(B,(C,D)));')
b = pt.Tree.from_string('((A,B),(C,D));')
a.treedist(b)

>0.0

tree1 = ete3.Tree('(A,(B,(C,D)));')
tree2 = ete3.Tree('((A,B),(C,D));')
tree1.compare(tree2)['norm_rf']
>0.5

Is this known?

Using version 1.5.5. MWE

import phylotreelib as pt
tree = pt.Tree.from_string("(Gorilla:3, (Human:2, (Chimpanzee:1, Bonobo:1):1):1);")
tree.numberprune(2, return_leaves=True)

Observed error:

>>> tree.numberprune(2, return_leaves=True)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.9/site-packages/phylotreelib.py", line 2192, in numberprune
    clusters = self.cluster_n(nclust=nkeep)[0]   # list containing sets of leafnames
  File "/usr/local/lib/python3.9/site-packages/phylotreelib.py", line 1825, in cluster_n
    kid_dict[kid].parent_height = pheight
AttributeError: 'Branchstruct' object has no attribute 'parent_height'