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niemasd / TreeSwift

TreeSwift: Fast tree module for Python 3
https://niema.net/TreeSwift
GNU General Public License v3.0
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Feature request: deroot #7

Closed bede closed 6 years ago

bede commented 6 years ago

Some software expects unrooted trees to have trifurcating roots. This would be a useful feature.

See Dendropy's deroot() http://dendropy.org/primer/treemanips.html?highlight=deroot#derooting

Source: https://github.com/jeetsukumaran/DendroPy/blob/7f2dfd2aad20daafb18b817b985d0146e670fc23/src/dendropy/datamodel/treemodel.py#L4810

niemasd commented 6 years ago

Added the feature in this commit: https://github.com/niemasd/TreeSwift/commit/ac354bb81f4463138663edf06d2bcc6c7bcfc1d5

I added it to TreeSwift 1.0.73, but for some reason it's not showing up via pip install yet. Hopefully PyPI will refresh shortly or something.

Basically, if the tree does not have a root edge (i.e., if tree.root.edge_length is None), nothing happens. If the tree does have a root edge (i.e., if tree.root.edge_length is not None), I create a new child of the root (by default, I label it "OLDROOT", but you can set it to whatever you want via the label argument of deroot()), I set its edge length to be what the root edge length was, and then I remove the root edge (i.e., I set tree.root.edge_length to None)

niemasd commented 6 years ago

Looks like 1.0.73 installs properly in pip now, so the updates should be accessible now!

bede commented 6 years ago

Fantastic! Amusingly I implemented this feature (albeit without modifying treeswift internals) early this morning, before checking my mail. Cheers : )