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Add hgvs parsing support for Range based SequenceLocations #381

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larrybabb opened this issue Apr 3, 2024 · 5 comments
Open

Add hgvs parsing support for Range based SequenceLocations #381

larrybabb opened this issue Apr 3, 2024 · 5 comments
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enhancement New feature or request priority:high High priority

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@larrybabb
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The current hgvs_tools.py does not consider the handling of hgvs expressions that have start or end Range values. I believe the biocommons/hgvs module support this but we are currently presuming the start/end is always an int.

@korikuzma korikuzma added enhancement New feature or request priority:high High priority labels Apr 4, 2024
@korikuzma
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korikuzma commented Apr 4, 2024

@larrybabb CNVs are for 50+ bp? What are the rules for Allele vs CNV?

@korikuzma
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@larrybabb CNVs are for 50+ bp? What are the rules for Allele vs CNV?

@larrybabb : Doesn't matter because user will choose the translator

@korikuzma
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@larrybabb what would you expect this allele to look like NC_000023.11:g.(31060227_31100351)_(33274278_33417151)dup?

@korikuzma
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@larrybabb :

Only want to support range for sequence locations used in copy number variation (CnvTranslator). Only support g. and m.

@korikuzma
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This was done in #387. Once the hgvs PR gets merged, we need to move these changes to main. I'll keep this issue open as a reminder

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enhancement New feature or request priority:high High priority
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