Modify filter_vep_transcript_csqs_expr so it can also accept hl.expr.StructExpression
#748
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…r.StructExpression
| if csqs is not None: | ||
| if "most_severe_consequence" not in csq_expr.dtype.element_type.fields: | ||
| fields = csq_expr if is_struct else csq_expr.dtype.element_type.fields | ||
| if "most_severe_consequence" not in fields: | ||
| logger.info("Adding most_severe_consequence annotation...") |
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This will actually get a different number of variants as the Browser, because they used ht.vep.most_severe_consequence directly. This function is getting less than the browser, is it because our CSQ_ORDER is updated?
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Like this: still using DRD2 as an example:
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That's why I used filter_vep_transcript_csqs_expr(ht.vep) in the toolbox
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From the notebook update in the toolbox:
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oh, sorry, I haven't seen the toolbox PR yet. One moment.
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The only one I'm not getting the same numbers for is Other, but I'm not sure why yet
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I figured out the other, I was being stupid. Will fix, but it's in the other PR
| @@ -860,19 +861,21 @@ def filter_vep_transcript_csqs( | |||
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| def filter_vep_transcript_csqs_expr( | |||
| csq_expr: hl.expr.ArrayExpression, | |||
| csq_expr: Union[hl.expr.StructExpression, hl.expr.ArrayExpression], | |||
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You add struct, considering if it's exploded?
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well, it can be used in the way we do for the toolbox because the annotation we are filtering on is top-level, or if it's exploded. Really any situation where the annotation you want to filter on isn't in a list
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