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Best way to traverse trees in phylesystem to get node dates #5

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snacktavish opened this issue Feb 21, 2020 · 2 comments
Open

Best way to traverse trees in phylesystem to get node dates #5

snacktavish opened this issue Feb 21, 2020 · 2 comments

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@snacktavish
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From Luna on gitter: the example code and pseudocode to get node ages from source trees
https://github.com/OpenTreeOfLife/python-opentree/blob/get-tree/examples/datelife.py
Specifically,
https://github.com/OpenTreeOfLife/python-opentree/blob/get-tree/examples/datelife.py#L39

Exporting as nexml and traversing in dendropy doesn't preserve annotations. Do we have nexson tree traversal code somewhere we should use?

@mtholder
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perhaps, but I just went ahead and wrote a nexson tree -> dendropy tree converter: #6

@mtholder
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I should mention that there are some assert some-condition-that-might-not-hold in that branch. I was just working through 1 nexson (tree3 from ot_1877). So that code will probably require some generalization for other studies/trees

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