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fix: lineage_to_clade missed a . #79

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merged 3 commits into from
Dec 15, 2023
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@corneliusroemer corneliusroemer commented Dec 14, 2023

Previous logic made HK.34 belong to HK.3, because the "comparison_lineage" was missing a trailing . in .startswith()

I've tried to add a unit test but I couldn't figure out how to get vscode to import the functions in the script from outside the script.

Previous logic made HK.34 belong to HK.3, because the "comparison_lineage" was missing a trailing `.` in `.startswith()`
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@jameshadfield jameshadfield left a comment

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Thanks @corneliusroemer!

If anyone's interested (or future me is interested), here are the steps I took to get a dataset to review:

  1. Find a Model run from GitHub's actions (and make sure it's for GISAID or open, as desired). E.g. this one
  2. Download the file (you may need to use the console link from the action to work out the filename). In this case it was nextstrain build --aws-batch --attach 7f2e4fa4-f8bb-44d3-a8c9-a9cbcee75ce0 --download results/gisaid/pango_lineages/global/mlr/model-outputs/2023-12-14_results.json
  3. Test locally, e.g. using Snakemake to run the relevant rule, or use -p and print it out so you can modify the output path as needed.
  4. If you need to visualise the output see the command in ./viz/README.md. While it differentiates clades & lineages, in reality the rendering depends on the JSON contents, so I used this to render the pango-lineages JSON from the master-branch JSON as "clades" vs the PR-branch JSON as "lineages" so I could compare them.

image

@jameshadfield jameshadfield merged commit d051c57 into main Dec 15, 2023
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@jameshadfield jameshadfield deleted the fix-lineage-to-clade branch December 15, 2023 02:31
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Thanks for testing! It seems to have worked first shot 🙃

Some CI could be helpful eventually for this but maybe not worth due to complexity (yet).

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2 participants