Adding functionalities to compute and plot frequencies of inversions

[jonbrenas]

Partially addresses #652 .

Created 2 functions inversions_frequencies and inversion_frequencies_advanced that should be compatible with other frequencies functions.

I still have to add tests (and they will be integration tests for now as we have not developed the simulated data for the karyotypes yet).

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Codecov Report

Attention: Patch coverage is 14.56954% with 129 lines in your changes missing coverage. Please review.

Project coverage is 93.56%. Comparing base (0197957) to head (1f09857).
Report is 19 commits behind head on master.

Files with missing lines	Patch %	Lines
malariagen_data/anoph/inversion_frq.py	13.42%	129 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #732      +/-   ##
==========================================
- Coverage   96.13%   93.56%   -2.57%     
==========================================
  Files          47       48       +1     
  Lines        4683     4834     +151     
==========================================
+ Hits         4502     4523      +21     
- Misses        181      311     +130     

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[31puneet]

Hi @jonbrenas
I have reviewed the PR and I found the following points:

1. Unit tests: I can modify simulate_snp_sites() inside conftest.py. The updated simulator will read the karyotype_tag_snps.csv from malariagen_data/resources, include the tag SNP coordinates (with valid REF/ALT alleles) into the generated Zarr arrays, enabling proper unit test coverage.
2. Code duplication: Both methods duplicate ~130 lines across the list vs str branches. Can be consolidated by normalizing input to a list upfront.
3. taxon_by bug: inversion_frequencies_advanced hardcodes "taxon" in the groupby instead of using the taxon_by parameter

I can push these changes or open a separate PR. What do you suggest ?

[jonbrenas]

You can go ahead and push to this branch.

[31puneet]

Hii @jonbrenas
I am not able to push directly to this branch as I got 403 permission denied error. Could you pull the changes ? Here is the link to my branch with the fixes and the new unit tests: https://github.com/31puneet/malariagen-data-python/tree/652-karyotype-frequencies

[31puneet]

Hi @jonbrenas PTAL

[jonbrenas]

Hi @31puneet, would it be possible to do it in a different branch instead of this one? This would probably make things easier.