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monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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Draw variants transcript and protein #148

Closed pnrobinson closed 2 months ago

pnrobinson commented 2 months ago

@ielis @lnrekerle This PR adds the drawing code as well as a test case for the VariantValidator response. The function, parse_response, line 157 of _vv.py, will also need to be changed -- to me it looks as if the code is expecting a different JSON structure from what we actually get -- I added the test case to understand the structure. Unless there is some other code that only passes part of the response, it is wrong PLEASE ADD DOCUMENTATION TO ALL FUNCTIONS LIKE THIS! It would be a lot easier to contribute code if the main assumptions and goals of each function were documented --

lnrekerle commented 2 months ago

The function, parse_response, line 157 of _vv.py, will also need to be changed -- to me it looks as if the code is expecting a different JSON structure from what we actually get -- I added the test case to understand the structure. Unless there is some other code that only passes part of the response, it is wrong PLEASE ADD DOCUMENTATION TO ALL FUNCTIONS LIKE THIS! It would be a lot easier to contribute code if the main assumptions and goals of each function were documented --

That function was originally written by @ielis, but I can take a look at it and see if I can recreate and fix the bug after this has been pushed. I do think that this PR as it is is ready to be pushed though. @pnrobinson

pnrobinson commented 2 months ago

I am going to merge this, and now the code seems to be working again. I am not changing _vv.py now but we may need to do so, but let's make that a separate PR