populationgenomics / automated-interpretation-pipeline

Rare Disease variant prioritisation MVP

MIT License

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Closed MattWellie closed 1 week ago

MattWellie commented 3 weeks ago

Fixes

Not sure if this is required, setting as a draft
I used to store HPO terms as a list of Strings. Recently this changed to HPO - Text Description. That packaging is going to make it harder to pull out just the HPO terms

Takes the list of compound Strings and changes it to a dictionary of {'HPO': 'Description'}
Later it should be pretty easy to pull out just the HPO terms if required for phenotype matching

cassimons commented 3 weeks ago

How would you feel about aligning with the {id: "HP:0012469", label: "Infantile spasms"} style format from phenopackets?

cassimons commented 1 week ago

Do you want this in now? Seems like a good idea to me.

MattWellie commented 1 week ago

Do you want this in now? Seems like a good idea to me.

Can do! Do your pheno-matching changes rely on this? The conflicts are wild, will try and clean that up

MattWellie commented 1 week ago

Crazy diff, get in the bin