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tree.prune incorrectly sets the branch length #4460

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diljotgrewal opened this issue Oct 18, 2023 · 1 comment · May be fixed by #4601
Open

tree.prune incorrectly sets the branch length #4460

diljotgrewal opened this issue Oct 18, 2023 · 1 comment · May be fixed by #4601

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@diljotgrewal
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Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

>>> import sys; print(sys.version)
3.7.16 (default, Jan 17 2023, 22:20:44)
[GCC 11.2.0]
>>> import platform; print(platform.python_implementation()); print(platform.platform())
CPython
Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-centos-7.9.2009-Core
>>> import Bio; print(Bio.__version__)
1.81

Expected behaviour

running prune function on diploid node of a tree that looks like this

Tree(rooted=False, weight=1.0)
    Clade(branch_length=0.0)
        Clade(branch_length=27.0, name='internal_3')
            Clade(branch_length=6.0, name='internal_6')
                Clade(branch_length=2.0, name='internal_4')
                    Clade(branch_length=1.0, name='cluster_13')
                    Clade(branch_length=3.0, name='cluster_39')
                Clade(branch_length=1.0, name='internal_5')
                    Clade(branch_length=2.0, name='cluster_7')
                    Clade(branch_length=2.0, name='cluster_8')
            Clade(branch_length=3.0, name='internal_2')
                Clade(branch_length=5.0, name='cluster_77')
                Clade(branch_length=1.0, name='internal_1')
                    Clade(branch_length=3.0, name='cluster_18')
                    Clade(branch_length=3.0, name='cluster_25')
        Clade(branch_length=0.0, name='diploid')

should result in

Tree(rooted=False, weight=1.0)
    Clade(branch_length=27.0, name='internal_3')
        Clade(branch_length=6.0, name='internal_6')
            Clade(branch_length=2.0, name='internal_4')
                Clade(branch_length=1.0, name='cluster_13')
                Clade(branch_length=3.0, name='cluster_39')
            Clade(branch_length=1.0, name='internal_5')
                Clade(branch_length=2.0, name='cluster_7')
                Clade(branch_length=2.0, name='cluster_8')
        Clade(branch_length=3.0, name='internal_2')
            Clade(branch_length=5.0, name='cluster_77')
            Clade(branch_length=1.0, name='internal_1')
                Clade(branch_length=3.0, name='cluster_18')
                Clade(branch_length=3.0, name='cluster_25')

Actual behaviour

the pruned tree looks like this

Tree(rooted=False, weight=1.0)
    Clade(name='internal_3')
        Clade(branch_length=6.0, name='internal_6')
            Clade(branch_length=2.0, name='internal_4')
                Clade(branch_length=1.0, name='cluster_13')
                Clade(branch_length=3.0, name='cluster_39')
            Clade(branch_length=1.0, name='internal_5')
                Clade(branch_length=2.0, name='cluster_7')
                Clade(branch_length=2.0, name='cluster_8')
        Clade(branch_length=3.0, name='internal_2')
            Clade(branch_length=5.0, name='cluster_77')
            Clade(branch_length=1.0, name='internal_1')
                Clade(branch_length=3.0, name='cluster_18')
                Clade(branch_length=3.0, name='cluster_25')

The branch length for node internal_3 is set to None in the pruned tree

Steps to reproduce

the python code is as follows:

while tree.count_terminals() > 0:
    altered = False
    for a in tree.get_terminals():
        if a.name == 'diploid':
            tree.prune(a)
            altered = True
    if not altered:
        break
@michaelfm1211
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michaelfm1211 commented Jan 23, 2024 •
edited

I know I'm about 3 months late to this, but it looks like this behavior is intentional:

biopython/Bio/Phylo/BaseTree.py

Lines 684 to 689 in df527d5

if parent == self.root:
# If we're at the root, move the root upwards
# NB: This loses the length of the original branch
newroot = parent.clades[0]
newroot.branch_length = None
parent = self.root = newroot

If this really is a problem, then maybe we can add a new keyword argument to the function to disable the newroot.branch_length = None part, however, I'm not sure if any other code in Bio.Phylo relies on the root having no length. Any thoughts on this?

@michaelfm1211 michaelfm1211 linked a pull request Jan 23, 2024 that will close this issue
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Preserve branch length in Phylo.TreeMixin.prune if keep_root_length=True michaelfm1211/biopython
2 participants
@diljotgrewal @michaelfm1211