Oql upstream downstream fusions in oncoprint #4494
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| @@ -5537,6 +5553,14 @@ export default class CBioPortalAPIInternal { | |||
| 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, | |||
| 'sampleMolecularIdentifiers0SampleId' ? : string, | |||
| 'structuralVariantFilter': StructuralVariantFilter, | |||
| 'structuralVariantQueries0Gene1ContainingOnlyOneIdentifierOrSpecialValue' ? : boolean, | |||
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seems kinda strange that there's index in this property name?
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This appears to be how Swagger exposes the docs for a list/array. The docs for the corresponding section look ok to me:
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This fixed with merge of the backend PR.
| */ | ||
| @computed get singleHugoGeneSymbols() { | ||
| if ( | ||
| this.urlWrapper.query.gene_list && |
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You can now use optional chaining to write this condition this.urlWrapper.query?.gene_list.length
it will evaluate falsy if gene_list is undefined
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Fix at all three places that his was done.
| return []; | ||
| } else { | ||
| const entrezGeneIds = genes |
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I think genes is, like 20k long, so perhaps we should have a computed lookup which is symbol to gene and then you can just iterate through structVarHugoGeneSymbols
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I think that genes is the genes that are derived from the query. There is a structure called referenceGenes that appears to represent all genes in the reference genome (~20k). However, I have I agree that this mapping would be more efficient with a looup. I have created a hugoGeneSymbol => Gene lookup and mapped from there.
src/shared/lib/oql/oqlfilter.ts
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| @@ -1205,6 +1242,23 @@ const getGeneFromAlterations = (q: SingleGeneQuery) => { | |||
| return (q.alterations as FUSIONCommandOrientationBase[])[0].gene; | |||
| }; | |||
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| export function fusionsInOQLQuery(oql_query: string): SingleGeneQuery[] { | |||
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curious why you switched to "fusion" here when everything else in PR is structural variant
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Ah good point, I have renamed these methods to the SV equivalent.
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This PR continues from #4413.
This PR depends on backend PR cBioPortal/cbioportal#9949
The new OQL syntax for SVs/fusions uses '::' notation. With this PR the OQL will show relevant tracks in Oncoprint.