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WIP: check pairwise vs sourmash compare output #366

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@ctb ctb commented Jun 20, 2024

This PR evaluates and compares the results of sourmash compare to the output of pairwise.

Specifically, it:

  • adds a directory, test_check_pairwise, containing a snakemake workflow;
  • this workflow uses both sourmash compare and pairwise from this plugin to calculate comparisons between the 64 podar-ref sketches.
  • the matrix output file is then converted into a "pairwise"-style CSV file, and a separate script compares the values to make sure they're the same/similar enough.

At least at the moment, the comparison is done only for the average_containment_ani column.

It is analogous to the gather check from https://github.com/ctb/2024-debug-gather-difference that we will add to this repo too, ref #363.

See sourmash-bio/sourmash#3134 for motivating inquiry ;)

TODO:

  • consider cleaning up code
  • consider joining forces with gather check
  • consider adding to CI

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