tree.infer_taxa() vs update_taxon_namespace()

[Yan Wong]

Using Dendropy 4, I've taken a tree and pruned branches off it, and now want to update the taxon namespace to include only the taxa left in the remaining tree. If I I use tree.infer_taxa() in DendroPy 4 I get a "CriticalDeprecationWarning", advising to use tree.update_taxon_namespace(). But as far as I can see, the new .

update_taxon_namespace() function doesn't delete unused taxa from a namespace: it only adds new ones to it.

What is the recommended way to refresh the namespace by deleting unused taxa but without using infer_taxa()?

Thanks

Yan

[Jeet Sukumaran]

Try: ``purge_taxon_namespace()``

> --
> You received this message because you are subscribed to the Google
> Groups "DendroPy Users" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to dendropy-user...@googlegroups.com
> <mailto:dendropy-user...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

--



--------------------------------------
Jeet Sukumaran
--------------------------------------
jeetsu...@gmail.com
--------------------------------------
Blog/Personal Pages:
http://jeetworks.org/
GitHub Repositories:
http://github.com/jeetsukumaran
Photographs (as stream):
http://www.flickr.com/photos/jeetsukumaran/
Photographs (by galleries):
http://www.flickr.com/photos/jeetsukumaran/sets/
--------------------------------------

[Yan Wong]

That's great. Thanks.