Skip to content

Supporting node_labels in as_nexus via translate #3435

@kaathewisegit

Description

@kaathewisegit

Nexus files support a translate directive in the trees block, which allows mapping short sample ids to full names. BEAST uses them, for example:

Begin trees;
	Translate
		   1 Gorilla,
		   2 Homo_sapiens,
		   3 Hylobates,
		   4 Lemur_catta,
		   5 M._fascicularis,
		   6 M._mulatta,
		   7 M._sylvanus,
		   8 Macaca_fuscata,
		   9 Pan,
		  10 Pongo,
		  11 Saimiri_sciureus,
		  12 Tarsius_syrichta
;
tree TREE1 = ((((((1:8.539364784844837,(2:5.97056745117597,9:5.97056745117597):2.5687973336688668):12.369406882406174,10:20.90877166725101):5.9847286187282265,3:26.893500285979236):21.11768348386113,((5:6.112091996272027,(6:1.9410612498662478,8:1.9410612498662478):4.171030746405778):4.238726956087251,7:10.350818952359278):37.66036481748109):17.830130560055792,11:65.84131432989616):20.354509510375422,(4:63.14102590761508,12:63.14102590761508):23.0547979326565):0.0;

Would tskit be open to adding this functionality to the as_nexus method? It could be implemented with a node_labels parameter (same as in as_newick). If it's present as_nexus would output a translation table for node ids present in node_labels

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions