discretise_mutations() in msprime_extras no longer works
hyanwong opened this issue · comments
Yan Wong commented
Not sure if we want to keep this function anyway, since it buggers up ARGweaver inference (and I've flagged it up as such). So eventually it either needs correcting or deleting by @jeromekelleher (not urgently though) as at the moment it triggers the bug below:
Traceback (most recent call last):
File "./src/plots.py", line 1682, in <module>
main()
File "./src/plots.py", line 1672, in main
args.func(cls, args)
File "./src/plots.py", line 1552, in run_setup
f.setup(args)
File "./src/plots.py", line 987, in setup
super().setup(args)
File "./src/plots.py", line 775, in setup
self.data = self.run_simulations(args.replicates, args.seed)
File "./src/plots.py", line 1026, in run_simulations
replicate_seed, replicate_seed, discretise_mutations=self.JeromesDiscretise)
File "./src/plots.py", line 876, in single_simulation
ts = msprime_extras.discretise_mutations(ts)
File "/Users/yan/Documents/Research/Wellcome/treeseq-inference/src/msprime_extras.py", line 93, in discretise_mutations
msprime.Mutation(position=x, node=mut.node, index=mut.index))
AttributeError: 'Mutation' object has no attribute 'node'
Yan Wong commented
We no longer discretise mutations in plots.py (we still do for ARGweaver, in ts_ARGweaver.py, but thats unavoidable)