remove-duplicates.bf seems to also remove tree annotations

[00-kelvin]

Hi there, I was attempting to use the remove-duplicates.bf tool on my tree and alignment before running the combined file through some hyphy analyses, but I noticed that the tree generated by remove-duplicates seems to lack the {Foreground} annotations that were in the tree before running it through the tool. I realized this when I tried running BUSTED on my combined tree/alignment file and got the following error:

Error:
'Foreground' is not a valid choice passed to 'Choose the set of branches to test for selection' ChoiceList using redirected stdin input or keyword arguments. Valid choices are
	All, Internal, Leaves, Unlabeled branches
 in call to ChoiceList(testSet, "Choose the set of branches to test for selection", 1, NO_SKIP, selectTheseForTesting);

(because my {Foreground} annotations were now gone)

Is there any way to use this tool without it getting rid of my annotations, or must annotations be added on after running the remove-duplicates tool? Thanks!

[spond]

Dear @00-kelvin,

Yes, the current implementation does remove annotations from branches. Easy enough to change; if you pull the latest repo, existing labels should be preserved.

Best,
Sergei

[00-kelvin]

Thank you very much, Sergei, I'll give the new version a try. I wanted to note while on the topic that the hyphy error-filter tool appears to have the same behavior -- I recently ran BUSTED on a number of genes with annotated Foreground branches, then used error-filter to extract the filtered alignment+tree, then tried to run BUSTED-PH on that filtered alignment (since I think BUSTED-PH is a better fit for my use case), but got the following error:

Error:
BUSTED-PH requires one or more designated branch subsets. in call to assert(ETqCuyBW.option_count>=2, error_msg);

etc.
If it would be just as easy to change that tool's implementation in the same way, I would be very grateful have that option! thank you again!

[spond]

Dear @00-kelvin,

Actually, now that you mentione it, error-filter does not even properly work when you apply BUSTED to a subset of tree branches (the sequences for NOT included in the test set will be output as blanks).

Let me add this to the list of things to fix in the next release.

Best,
Sergei