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naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
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Taxon names with parentheses in database #76

Closed hettling closed 9 years ago

hettling commented 9 years ago

I stumbled across a frog species name which contains parentheses: Hylarana (Papuarana) sp. FB-2006. Checking in the database, there are some more. Both Figtree and Bio::Phylo get problems when these names end up in a newick string.

rvosa commented 9 years ago

It would be good if taxize had a flag to filter out "weird" names (maybe anything that's not a binomial or something)? Op Mon, 3 Aug 2015 om 13:17 schreef hettling notifications@github.com

I stumbled across a frog species name which contains parentheses: Hylarana (Papuarana) sp. FB-2006. Checking in the database, there are some more. Both Figtree and Bio::Phylo get problems when these names end up in a newick string.

— Reply to this email directly or view it on GitHub https://github.com/naturalis/supersmart/issues/76.

hettling commented 9 years ago

Using only binomial taxon names is now a taxize option: 039679bf36b82d66239f84a37680f962900bc287

If the user decides not to use this option, parentheses (and also underscore) are encoded into e.g. |smrt:parenthesisopen|. and decoded again when used for database querying.