Ability to export branch labels

[jameshadfield]

Currently there is no ability for augur export v2 to export custom branch labels.

In general, node-data.json defines traits for nodes via the following structure,

{
    "nodes": {
        "NODE_NAME": {
            "TRAIT_NAME": "VALUE"
        }
    }
}

which augur export v2 maps onto nodes as such:

"NODE_NAME": {
    "node_attrs": {
        "TRAIT_NAME": {
            "value": "VALUE"
        },
    }
}

There are two "special-case" situations which are relevant here:

1. if TRAIT_NAME == "clade_annotation" then augur will export this as a branch label rather than a node_attr. "clade_annotation" is typically produced by augur clades and is how we get clade labelling in most of our datasets.

2. augur export v2 automatically creates a branch label for "aa" if a node-data file with "aa_muts" is provided.

These two cases are the only time that augur export adds information to the branch_attrs of a node. This means that there is no ability for augur export v2 to set custom branch labels for (internal) nodes.

[jameshadfield]

One implementation would be to look for a top-level "branch_labels" key in the node-data JSON. For instance, we could modify augur clades to produce something like

"nodes": {
    "NODE_0000549": {
           "clade_membership": "20A"
    }
},
"branch_labels": {
    "NODE_0000549": {
          "clade": "20A",
    }
}

This would imply that augur clades had additional arguments along the lines of

augur clades --name clade_membership --root-label clade

Which would remove the need for augur export v2 to special case "clade_annotation" as well as allowing custom branch labels from arbitrary node-data inputs.