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Newick label generation should be invertible #76

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jar398 opened this issue Apr 7, 2016 · 0 comments
Open

Newick label generation should be invertible #76

jar398 opened this issue Apr 7, 2016 · 0 comments

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@jar398
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jar398 commented Apr 7, 2016

It would be nice if the mapping between strings and newick labels (in newick generated by treemachine and taxomachine) were invertible. Quotation takes care of this for the most part, but currently, underscore is treated the same as space, and mapped to _ when not quoted, so there is no way to regenerate the distinction when the label is converted back to a string.

To get invertibility, we would have to treat _ as a character that needs to be quoted (since otherwise both space and _ would go to _). Currently it's treated as non-special. At that point the other analysis applies: either we have Foo_ott123 and 'Foo+ ott123', or we have 'Foo_ott123' and 'Foo+_ott123'. I have not yet done anything about this.

This issue was split off from OpenTreeOfLife/treemachine#131 .

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