Unable to extract assigned color, clade id, and leaf id into tsv/dataframe

[evogytis]

Unable to extract assigned color, clade id, and leaf id into tsv/dataframe

[evogytis]

Hi Celeste,

The error is saying that your tree does not contain any internal nodes (k.is_node()) whose parent node has a trait called type ('type' in k.parent.traits) and whose state is different from its parent's (k.traits['type']!=k.parent.traits['type']). Did you collapse some branches of the tree using collapse_target by any chance? If so, then all the nodes matching that condition will have been removed and so won't exist and won't be found in the modified tree.

You'd also have issues assigning clade ID to the tips since for elem in K: is trying to iterate over a variable that wan't defined (k would be a node if the condition above succeeded but K has not been mentioned previously). Likewise for element - only elem is defined.

The way you would achieve what you want is something like

for elem in k.leaves: ## this iterates over a list of node's descendant tip names
    print(f'{elem}\t{clade_id}')

Since this is not a bug but a use case I'll close this issue. If you have further questions about using baltic please direct them to my email.