Fix branch length annotation #908
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Sets branch length to the difference in divergence between each node and its parent instead of setting the cumulative branch length from the root of the tree. Auspice JSONs store the cumulative branch length for easier plotting in Auspice, but when we import the JSON into Python as a tree, the branch length should not be cumulative. Since this cumulative branch length is useful on its own and also required for calculating the actual branch length (in the current recursive implementation of `json_to_tree`, at least), this commit adds a `cumulative_branch_length` attribute to each node of the tree produced by `json_to_tree` and passes this value as a new optional argument to recursive calls. We should really reimplement this function as a non-recursive function, though. See the cartography script for annotating Auspice JSONs [1], for an example of this kind of non-cursive implementation. Fixes #714 [1] https://github.com/blab/cartography/blob/master/notebooks/scripts/annotate_tree.py
Codecov Report
@@ Coverage Diff @@
## master #908 +/- ##
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+ Coverage 34.63% 34.66% +0.03%
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Files 42 42
Lines 6006 6009 +3
Branches 1538 1539 +1
==========================================
+ Hits 2080 2083 +3
Misses 3853 3853
Partials 73 73
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rneher
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Description of proposed changes
Sets branch length to the difference in divergence between each node and its parent instead of setting the cumulative branch length from the root of the tree. Auspice JSONs store the cumulative branch length for easier plotting in Auspice, but when we import the JSON into Python as a tree, the branch length should not be cumulative. Since this cumulative branch length is useful on its own and also required for calculating the actual branch length (in the current recursive implementation of
json_to_tree, at least), this commit adds acumulative_branch_lengthattribute to each node of the tree produced byjson_to_treeand passes this value as a new optional argument to recursive calls.We should really reimplement this function as a non-recursive function, though. See the cartography script for annotating Auspice JSONs, for an example of this kind of non-cursive implementation.
Related issue(s)
Fixes #714
Testing