SACGF / SACGF/variantgrid

HGVS resolution method should also include whether we used transcript/genome sequence

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#872 1 comment 0 reactions 0 assignees View on GitHub
enhancement Reference base
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Python
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Description

Biocommons HGVS implementation can now use Transcript sequences instead of pasting together exons from the genome

This can affect the reference base pulled up (and thus also normalization) - so depending if the local system has the transcript or now it will change how things resolve. We should store this

The implementation is DjangoTranscriptDataProvider used to use SingleBuildFastaSeqFetcher (which calls cdot.FastaSeqFetcher) but now we use ChainedSeqFetcher to call DBTranscriptSeqFetcher first (and die if we don't have it). These have a "source" attribute to tell them apart

I'm not sure if there's actually a way to tell which one is used during a lookup with the current chaining system. It's probably quite difficult as it's called by biocommons HGVS internals - maybe set a global variable on ChainedSeqFetcher object to record what was last used

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