Add filter_vep_transcript_csqs_expr, a version of filter_vep_transcript_csqs that takes and returns an ArrayExpression
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| mane_select: bool = False, | ||
| filter_empty_csq: bool = True, | ||
| ensembl_only: bool = True, | ||
| filter_empty_csq: bool = True, |
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Thoughts on updating to remove_empty_csq ?
Suggested change
| filter_empty_csq: bool = True, | |
| remove_empty_csq: bool = True, |
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Looks like we'd only need to update gnomad_qc in one place and then there would be a bulk replace in your other VEP PR. I just think remove is more clear since filter is a bit overloaded and can be ambiguous as to whether you are keeping or removing the filtered material.
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I think it makes sense to do it in it's own PR where that is all that is done since it's not a name introduced in this PR, and it is technically a breaking change
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| Filter VEP transcript consequences based on specified criteria, and optionally filter to variants where transcript consequences is not empty after filtering. | ||
| If `filter_empty_csq` parameter is set to True, the Table/MatrixTable is filtered | ||
| to variants where 'transcript_consequences' within the VEP annotation is not empty | ||
| after the specified filtering criteria is applied. | ||
| .. note:: | ||
| By default, the Table/MatrixTable is filtered to variants where | ||
| 'transcript_consequences' within the VEP annotation is not empty after filtering | ||
| to Ensembl canonical transcripts with a most severe consequence of | ||
| 'synonymous_variant'. |
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Suggested change
| Filter VEP transcript consequences based on specified criteria, and optionally filter to variants where transcript consequences is not empty after filtering. | |
| If `filter_empty_csq` parameter is set to True, the Table/MatrixTable is filtered | |
| to variants where 'transcript_consequences' within the VEP annotation is not empty | |
| after the specified filtering criteria is applied. | |
| .. note:: | |
| By default, the Table/MatrixTable is filtered to variants where | |
| 'transcript_consequences' within the VEP annotation is not empty after filtering | |
| to Ensembl canonical transcripts with a most severe consequence of | |
| 'synonymous_variant'. | |
| Filter VEP transcript consequences based on specified criteria, and optionally remove variants where transcript consequences is empty after filtering. | |
| If `remove_empty_csq` parameter is set to True, the Table/MatrixTable is filtered | |
| to variants where 'transcript_consequences' within the VEP annotation is not empty | |
| after the specified filtering criteria is applied. | |
| .. note:: | |
| By default, the Table/MatrixTable is filtered to variants where | |
| 'transcript_consequences' within the VEP annotation is not empty after filtering | |
| to Ensembl canonical transcripts with a most severe consequence of | |
| 'synonymous_variant'. |
If the above suggestion is accepted.
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| :param filter_empty_csq: Whether to filter out rows where 'transcript_consequences' | ||
| is empty, after filtering 'transcript_consequences' to the specified criteria. | ||
| Default is True. |
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Suggested change
| :param filter_empty_csq: Whether to filter out rows where 'transcript_consequences' | |
| is empty, after filtering 'transcript_consequences' to the specified criteria. | |
| Default is True. | |
| :param remove_empty_csq: Whether to remove rows where 'transcript_consequences' | |
| is empty, after filtering 'transcript_consequences' to the specified criteria. | |
| Default is True. |
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Dependent on arg rename suggestion
| } | ||
| t = t.annotate_rows(**vep_data) if is_mt else t.annotate(**vep_data) | ||
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| if filter_empty_csq: |
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Suggested change
| if filter_empty_csq: | |
| if remove_empty_csq: |
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Same comment as above
mike-w-wilson
approved these changes
Jul 8, 2024
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