What is the best way to perform root-to-tip analysis using
treetime, and export the molecular clock outliers that are flagged during the process?
I’m trying to use the
treetime Python package for that, using a script to export the data processed int he lines below, but I’ve not been able to get
treetime to run on python.
tt.clock_filter(reroot=reroot, n_iqd=clock_filter_iqd, plot=False)
leaves = [x for x in tt.tree.get_terminals()]
for n in leaves:
this should work. what is the problem you are running into?
I was getting an error message:
raise MissingDataError("ERROR: ALMOST NO VALID DATE CONSTRAINTS")
The TSV file I was using had
date columns. Not sure what was wrong, but I guess I need to convert dates from
YYYY-MM-DD into numerical format, using
augur refine does. But I’m not sure if that is the solution.
I switched to the standalone
treetime installation, and figured out that the output
dates.tsv lists all the outlier with their dates as “
--”. So, I managed to get the list of molecular clock outliers in that way.