incorrect json -> Bio.Phylo conversion #714
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huddlej
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Apr 27, 2022
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
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Apr 28, 2022
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The utility function
json_to_treedoes not correctly calculates branch length. Instead of calculating the difference between divergence of parent and child node, it simply assigns divergence:https://github.com/nextstrain/augur/blob/master/augur/utils.py#L589
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