feat: Address deletion and substitution bugs in gnomad_vcf_to_protein_variation.py#646
feat: Address deletion and substitution bugs in gnomad_vcf_to_protein_variation.py#646jarbesfeld wants to merge 4 commits intostagingfrom
gnomad_vcf_to_protein_variation.py#646Conversation
korikuzma
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korikuzma
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Didn't review changes (just want to link to resources if they exist)
| cdk11a_e314del, | ||
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| """Test that deletion queries return correct response""" | ||
| # Reading Frame 0, Positive Strand (CA3250144726) |
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@katie-perry This is the describing the reading frame. We used 0-indexing to describe the possible reading frames, but the options here would be 0,1,2 depending on where in the codon the deletion occurs
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do we have any examples we could add for 1? Aside from that, the PR looks good to me
| cdk11a_e314del, | ||
| ): | ||
| """Test that deletion queries return correct response""" | ||
| # Reading Frame 0, Positive Strand (CA3250144726) |
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do we have any examples we could add for 1? Aside from that, the PR looks good to me
katie-perry
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revoking my approval for now - I think we should explore a solution earlier in the workflow where we may not need different branching logic depending on the reading frame, if at all possible! I'm going to look into this today
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Closing this PR as the fix is being implemented in Katie's PR |
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closes #447
Not entirely sure why my reading frame change works, but would like to test with other known cases if possible