VS 396 clinvar grabs too many values #7823
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## ah_var_store #7823 +/- ##
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Coverage ? 51.397%
Complexity ? 26413
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Files ? 2170
Lines ? 164837
Branches ? 17775
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Hits ? 84721
Misses ? 74715
Partials ? 5401 |
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gbggrant
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May 3, 2022
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| def test_clinvar_inclusion(self): | ||
| clinvar_swap = [{ 'id': 'RCV01', \ |
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Do you want to add a test case for a case where the id does NOT start with 'RCV'?
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Yes and I think that line 88 should handle that case
mcovarr
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May 3, 2022
| @@ -143,6 +143,7 @@ def get_gnomad_subpop(gnomad_obj): | |||
| max_an = None | |||
| max_af = None | |||
| max_subpop = "" | |||
| ## TODO will there ever be unexpected values in gnomad_subpop (values not in gnomad_ordering) ? | |||
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Is this TODO more like "defend against possible unexpected values appearing in gnomad_subpop"?
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yes I think that's a good distinction
| row["clinvar_classification"] = ordered_significance_values # special sorted array | ||
| updated_dates.sort(key=lambda date: datetime.strptime(date, "%Y-%m-%d")) # note: method is in-place, and returns None | ||
| row["clinvar_last_updated"] = updated_dates[-1] # most recent date | ||
| row["clinvar_phenotype"] = sorted(phenotypes) # union of all phenotypes |
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indent inconsistency issues
scripts/variantstore/wdl/extract/create_variant_annotation_table.py
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| ordered_significance_values.extend(values_not_accounted_for) # add any values that aren't in significance_ordering to the end | ||
| row["clinvar_id"] = clinvar_ids # array | ||
| row["clinvar_classification"] = ordered_significance_values # special sorted array | ||
| updated_dates.sort(key=lambda date: datetime.strptime(date, "%Y-%m-%d")) # note: method is in-place, and returns None |
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thank you for the comment, I forget that every time I've been away from Python for a while and it never fails to bite me 🙂
…le.py Co-authored-by: Miguel Covarrubias <[email protected]>
…gatk into rc-vs-396-clinvar-greedy
This was referenced Mar 17, 2023
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currently clinvar grabs all values in the variants section of the annotation json---this is wrong because nirvana includes clinvar values from all overlapping variants.
this change limits the clinvar values to the correct variant only
and tests the change as well