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Add cohort_allele_frequencies method #729 #777

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merged 2 commits into from
Jan 22, 2022
Merged

Add cohort_allele_frequencies method #729 #777

merged 2 commits into from
Jan 22, 2022

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timothymillar
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Fixes #729

@timothymillar timothymillar mentioned this pull request Dec 9, 2021
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jeromekelleher
jeromekelleher reviewed Dec 9, 2021
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LGTM, one question about the NaN corner case semantics though.

sgkit/stats/aggregation.py Outdated
variables.validate(ds, {cohort_allele_count: variables.cohort_allele_count_spec})
AC = ds[cohort_allele_count]
K = AC.sum(dim="alleles")
# avoid divide by zero
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Should we be returning 0 in this case or NaNs? I think in other stats we decided it was simpler to let the maths libraries decide what the outcome of a 1/0 should be, but to suppress the warnings.

We should be consistent with the behaviour of the popgen stats here I think.

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AFAIK runtime warnings still can't be suppressed in Dask. I'll just let them be raised and suppress them in the tests where needed (as in Tajima's D).

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Thanks for the review @jeromekelleher

jeromekelleher
jeromekelleher approved these changes Dec 10, 2021
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LGTM!

@tomwhite tomwhite added the auto-merge Auto merge label for mergify test flight label Dec 13, 2021
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Looks like this is causing an existing test to fail.

@timothymillar
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@tomwhite I think the test failure was due to #778 which was unrelated (change upstream). Can you restart the builds?

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@tomwhite I think the test failure was due to #778 which was unrelated (change upstream). Can you restart the builds?

Yes, that looks like it was the problem. I can't see a button to re-run the build - maybe try rebasing?

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codecov-commenter commented Jan 22, 2022 •
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Codecov Report

Merging #777 (dbc9864) into main (881555a) will not change coverage.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff            @@
##              main      #777   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           36        36           
  Lines         3050      3057    +7     
=========================================
+ Hits          3050      3057    +7
Impacted Files Coverage Δ
sgkit/__init__.py 100.00% <ø> (ø)
sgkit/stats/aggregation.py 100.00% <100.00%> (ø)
sgkit/variables.py 100.00% <100.00%> (ø)

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@mergify mergify bot merged commit d5187c9 into sgkit-dev:main Jan 22, 2022
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Cohort allele frequencies
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@timothymillar @tomwhite @codecov-commenter @jeromekelleher