sgkit
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Link between variable and function to compute it
There doesn't seem to be any link between variables, and how they are computed either in the documentation, or in error messages. For example, I want to get variant_allele_frequency
which I can search for in the docs and I find the spec, but this doesn't tell me that I need to call variant_stats
to compute it. If I access the variable, I just get an error
get_prob_dist(ds)
File "/scratch/jk/work/github/sgkit-publication/src/collect_data.py", line 37, in get_prob_dist
af = ds.variant_allele_frequency.values[:, 1]
File "/home/jk/.local/lib/python3.9/site-packages/xarray/core/common.py", line 278, in __getattr__
raise AttributeError(
AttributeError: 'Dataset' object has no attribute 'variant_allele_frequency'
It would be nice if the error message told me "you need to call sg.variant_stats(ds)
Likewise, I was looking at call_dosage
, which I could find no documentation on.
I wonder if there's some sort of automatic annotation we could add to variables that would help with this?
@ravwojdyla I seem to remember you were thinking about things like this before??