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Add modular genotype & variant ingests #590

Merged
merged 4 commits into from
Jun 12, 2024
Merged

Add modular genotype & variant ingests #590

merged 4 commits into from
Jun 12, 2024

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kevinschaper
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  • add script fix for mesh: prefix in mondo.sssom.tsv
  • Adds genotype & variant ingests. Uses ingets.yaml & ingest transform cli code as a way to handle pass-through ingests by configuration. (plus small tweak to mesh->MESH fix).

@kevinschaper kevinschaper marked this pull request as ready for review June 11, 2024 17:03
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Tagging everyone here as reviewers to see how the modular ingests are getting hooked up to the kg build process right now. This is a really minimal solution, in particular because it doesn't have any kind of filtering support.

Longer term, we should either add the filtering support to cat-merge (maybe even using the kgx merge config format), or we should set up Koza to take biolink model class names to define both the input columns and the output columns, and have a sort of pass-through mode where the transform step just iterates over each row and the Koza filter code in the reader can be used.

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@amc-corey-cox amc-corey-cox left a comment

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Yeah, this looks great. Thanks for having me take a look Kevin.

@kevinschaper kevinschaper merged commit 8840883 into main Jun 12, 2024
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@kevinschaper kevinschaper deleted the merge-modulars branch June 12, 2024 16:03
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3 participants