Add generic constraint functions - annotate_mutation_type(), trimer_from_heptamer(), collapse_strand(), add_most_severe_csq_to_tc_within_vep_root() #474
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since there are only three functions here you can add the names of them in the title of this PR to be more descriptive (there will also probably be future PRs moving over more of the generic constraint functions so it's helpful to have a little more detail in the titles) |
gnomad/utils/constraint.py
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| from gnomad.utils.vep import add_most_severe_consequence_to_consequence | ||
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| def annotate_variant_types( |
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there's a similarly named function with a different definition for variant_type here:
gnomad_methods/gnomad/utils/annotations.py
Line 751 in b3f960b
so i would suggest changing the function name, maybe "annotate_mutation_type" and change below instances of "variant_type" to "mutation_type"....these names are very similar but it might at least help clear up some confusion
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Does any place in pipeline use 'variant_type'? I can't find any.
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looks like it was mostly used for plotting purposes
this comment still needs to be resolved |
gnomad/utils/constraint.py
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| - variant_type_model | ||
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| :param t: Input Table or MatrixTable. | ||
| :param trimer: Whether to use trimers for context. Defaults to False (uses heptamers as context). |
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If trimer is set to true here, but the context is actually formatted as a heptamer within the ht/mt this function wouldn't behave as expected. I think it's actually safer to drop this parameter and within the function set the mid_index by first checking the length of context to see if it is formatted as a trimer or a heptamer.
gnomad/utils/constraint.py
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| from gnomad.utils.vep import add_most_severe_consequence_to_consequence | ||
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| def annotate_variant_types( |
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looks like it was mostly used for plotting purposes
averywpx
changed the title
Add generic functions that were in
gnomad_lofrepo.