feat!: add more support for queries in gnomad_vcf_to_protein #529
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korikuzma
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enhancement
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@korikuzma we should consider asking @ahwagner to review as well to confirm. |
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Since this endpoint needs gene-normalizer data, I'm wondering if we should use ProteinSequenceConsequence. Right now, I have the catvar pydantic models in metakb (it made development easier). Maybe we should move them here or in a different place? |
| """Define response for gnomad vcf to protein service""" | ||
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| gene_context: Optional[core_models.Gene] = None | ||
| vrs_ref_allele_seq: Optional[StrictStr] = None |
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I could have just added this to variation extensions field, but thought it'd be easier for varcat if we had a field to retrieve
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I am always pro making varcat better (easier to develop). @ahwagner any objections?
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Yes, this is good info to include. I would like there to be a gene_context field on the VRS 2.x SequenceReference class but it doesn't exist yet, so we can leave that as a downstream issue.
Hmm. I will default to where @ahwagner thinks is best for them since he runs the whole show. |
* Updates cool-seq-tool + ga4gh.vrs versions. This mainly had to do with fixing inter-residue positions. cool-seq-tool previous versions returned 0-based coordinates. * Temporarily removes gnomad_vcf_to_protein, which will be added back in #529
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@ahwagner Do you have time to review this? |
| """Define response for gnomad vcf to protein service""" | ||
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| gene_context: Optional[core_models.Gene] = None | ||
| vrs_ref_allele_seq: Optional[StrictStr] = None |
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Yes, this is good info to include. I would like there to be a gene_context field on the VRS 2.x SequenceReference class but it doesn't exist yet, so we can leave that as a downstream issue.
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@korikuzma I am pretty sure I have reviewed this at least once if not more. Is there any reason for me to review again? |
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
@wesleygoar no, when changes get made the reviews are dismissed. I only re-request reviews when I need things to be reviewed again. |
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
close #362
@wesleygoar still in draft, but your feedback would be nice