feat!: add assembly registry utilities#63
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jsstevenson merged 4 commits into0.2.0from Oct 21, 2025
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korikuzma
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Oct 21, 2025
| HG19 = "hg19" | ||
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| ID_TO_REFERENCE_MAP = { |
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Consider changing from set to a list. I'm thinking of the case where want to do a quick look up without SeqRepo, where we know both the assembly and chromosome so we could do something like ID_TO_REFERENID_TO_REFERENCE_MAP["hg19"][11-1]
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Yeah that seems ok. I was wondering about whether we'd need to add more IDs in the future, but now that I think about it, I'm not sure what those would be.
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* Add get_assembly_from_refget_id(), which takes a "SQ.ABCDEFG"-type string and checks against a static mapping of known sequence IDs and their corresponding reference assemblies. In our other use cases, we use SeqRepo for this, but it seems silly to do so when there's a pretty small number of possible associations and they rarely (never?) change. This will enable applications like AnyVar to unit-test liftover protocols without needing to mock or stage a seqrepo interface. * Tighten requirements on input. I think it's more complicated than it's worth to be flexible about whether something is a string or an enum. Previously we might've left this in to be compatible with pyliftover but I think we can afford to be stricter. * update various docs/docstring type things This breaks some interface elements. I'm merging it into a 0.2.0 branch because I think there are one or two other small changes I'd like to make before assessing the impact of a release on places like coolseqtool.
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close #62
get_assembly_from_refget_id(), which takes a"SQ.ABCDEFG"-type string and checks against a static mapping of known sequence IDs and their corresponding reference assemblies. In our other use cases, we use SeqRepo for this, but it seems silly to do so when there's a pretty small number of possible associations and they rarely (never?) change. This will enable applications like AnyVar to unit-test liftover protocols without needing to mock or stage a seqrepo interface.pyliftoverbut I think we can afford to be stricter.This breaks some interface elements. I'm merging it into a
0.2.0branch because I think there are one or two other small changes I'd like to make before assessing the impact of a release on places like coolseqtool.