pyslim
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tskit-dev
Tools for dealing with tree sequences coming to and from SLiM.
Hello, I am running two simulations on slim which differ only by the number of burn in generations, one has 500,000 and the other 10,000, and my tree recording starts...
Currently the default `sex_ratio` in population metadata (used for WF models with separate sexes) [is 0.0](https://github.com/tskit-dev/pyslim/blob/b209ac2028ba09d45219adfba20606902c2b1da0/pyslim/slim_metadata.py#L351). This was the source of some confusion [on the SLiM email list](https://groups.google.com/g/slim-discuss/c/6OhOVWhFYGw/m/HxPBFKdgAQAJ?utm_medium=email&utm_source=footer&pli=1). This seems...
The list at https://tskit.dev/pyslim/docs/latest/python_api.html#python-api does not include some methods, eg `next_slim_mutation_id`.
At the moment the tutorial.html page says: "At time of writing, we don’t have a built-in allele_frequency method, so we’ll use the following snippet" But now we have `Variant.frequencies()`: ```python...
Say you want to output something about individuals within SLiM (say, a tag that is not stored in metadata, or a computed, random phenotype), and match it up to the...
I _think_ this might actually be a `tskit` problem, but I stumbled across it in a `pyslim` context so I thought I'd report here first, and we can escalate to...
For next time: (*note:* update from https://github.com/popsim-consortium/stdpopsim/issues/1565) - [ ] - make sure you're on main - [ ] - increment the version in pyslim/_version.py - [ ] - update...
... there may be problems with individuals having `-1` populations Note that in the tutorial the first example in the tutorial gets you haploid individuals and no population; this produces...
... or probably just update `annotate_tables` to actually do this right when existing mutations aren't already in SLiM format. In @Tatianabellagio's example, trying to use `annotate_tables` produces a metadata schema...
As pointed out by @Tatianabellagio, this produces an assertion error when trying to run `annotate_tables` on a tsinferred tree sequence. I'm not sure if this is a bad thing by...