Add option to exclude polyphen from process consequences #685
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gnomad/utils/vep.py
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| vep_root: str = "vep", | ||
| penalize_flags: bool = True, | ||
| csq_order: Optional[List[str]] = None, | ||
| has_polyphen_sift: bool = False, |
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Since sift isnt involved, lets just make this has_polyphen and it should default to True or else this is a breaking change which we should avoid when possible.
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I will add a note in VEP 105, all the release HT won't have polyphen, we have to set this to False.
| flag_condition = (tc.lof == "HC") & (tc.lof_flags != "") | ||
| modifier -= hl.if_else(flag_condition, flag_score, no_flag_score) | ||
| modifier -= hl.if_else(tc.lof == "OS", 20, 0) | ||
| modifier -= hl.if_else(tc.lof == "LC", 10, 0) |
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Just curious, why did you move away from the case statement here?
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I wanted to keep the previous structure, but if I add if in, it will be a bit redundant, so I worked with chatGPT for a few rounds to simplify it.
gnomad/utils/vep.py
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| csqs = hl.literal(csq_order) | ||
| csq_dict = hl.literal(dict(zip(csq_order, range(len(csq_order))))) | ||
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| def csq_score(tc: hl.expr.StructExpression) -> int: |
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I think we should make these "private" with a _ prefix since they only make sense inside this function. We haven't always done this through the repo, this function included but I think its a helpful thing to add.
gnomad/utils/vep.py
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| flag_score = 500 | ||
| no_flag_score = flag_score * (1 + penalize_flags) | ||
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| def csq_score_modifier(tc: hl.expr.StructExpression) -> float: |
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Same comment as above -> _csq_score_modifier
Co-authored-by: Mike Wilson <[email protected]>
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I can't pass check for the "note", so I moved them before. Is it Okay? |
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This change makes an option to not use polyphen_prediction in csq_order and its prioritization score. Test on vep_context 105.