use matched_effect_allele

PGScatalog / pgscatalog_utils

(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files

Apache License 2.0

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use matched_effect_allele #7

Closed nebfield closed 2 years ago

smlmbrt commented 2 years ago

Should it not reference matched_effect_allele on lines 37-44 of pgscatalog_utils/match/postprocess.py to count unique matches?

smlmbrt commented 2 years ago

I think maybe _label_biallelic_ambiguous might be out of date as well. Since it's bi-allelic you could just:

Complement REF
Check if REF_FLIP == ALT

smlmbrt commented 2 years ago

Should it not reference matched_effect_allele on lines 37-44 of pgscatalog_utils/match/postprocess.py to count unique matches?

Hmmmm, actually maybe that is fine because it's aggregating over the matches to an original variant... but then maybe the assertion has to be (distinct.groupby(['accession', 'ID']).count()['count']) == 1) to make sure that more than 1 variant from the score didn't match to the same variant?