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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| import { describe, expect, test } from '@jest/globals' | ||
|
|
||
| import { | ||
| resolveVACohortAlleleFrequencies, | ||
| resolveVAAllele, | ||
| Allele as VAAllele, | ||
| CohortAlleleFrequency, | ||
| } from './va' | ||
|
|
||
| const alleleEsDocument = { | ||
| vrs: { | ||
| ref: { | ||
| allele_id: 'ga4gh:SQ.IAmTheRefStateID', | ||
| start: 123, | ||
| end: 234, | ||
| state: 'G', | ||
| }, | ||
| alt: { | ||
| allele_id: 'ga4gh:SQ.IAmTheAltStateID', | ||
| start: 124, | ||
| end: 235, | ||
| state: 'A', | ||
| }, | ||
| }, | ||
| } | ||
|
|
||
| const expectedAllele: VAAllele = { | ||
| _id: 'ga4gh:SQ.IAmTheAltStateID', | ||
| type: 'Allele', | ||
| location: { | ||
| _id: 'ga4gh:VSL.OogSNIt-1Z7HF4tbdm45IDLYc7-oSE2Y', | ||
| type: 'SequenceLocation', | ||
| sequence_id: '2mN7PzLXx-QQq2GVIODPRSkWmlwybsv0', | ||
| interval: { | ||
| type: 'SequenceInterval', | ||
| start: { type: 'Number', value: 124 }, | ||
| end: { type: 'Number', value: 235 }, | ||
| }, | ||
| }, | ||
| state: { | ||
| type: 'LiteralSequenceExpression', | ||
| sequence: 'A', | ||
| }, | ||
| } | ||
|
|
||
| describe('resolveVAAllele', () => { | ||
| test('parses a single allele correctly', async () => { | ||
| const resolved = await resolveVAAllele(alleleEsDocument, null, null) | ||
| expect(resolved).toEqual(expectedAllele) | ||
| }) | ||
| }) | ||
|
|
||
| describe('resolveVACohortAlleleFrequency', () => { | ||
| const exomeEsDocument = { | ||
| ac: 5, | ||
| an: 100, | ||
| hemizygote_count: 2, | ||
| homozygote_count: 3, | ||
| faf95: { popmax: 0.123, popmax_population: 'afr' }, | ||
| ancestry_groups: [], | ||
| } | ||
|
|
||
| const variantESDocument = { | ||
| ...alleleEsDocument, | ||
| variant_id: '1-123-G-A', | ||
| exome: exomeEsDocument, | ||
| joint: { fafmax: { faf95_max: 0.234, faf95_max_gen_anc: 'amr' } }, | ||
| } | ||
|
|
||
| test('parses a single CohortAlleleFrequency correctly', async () => { | ||
| const resolved = await resolveVACohortAlleleFrequencies(variantESDocument, null, null) | ||
| const expected: CohortAlleleFrequency[] = [ | ||
| { | ||
| id: 'gnomad4:1-123-G-A', | ||
| label: 'Overall Cohort Allele Frequency for 1-123-G-A', | ||
| type: 'CohortAlleleFrequency', | ||
| focusAllele: expectedAllele, | ||
| derivedFrom: { | ||
| id: 'gnomad4.1.0', | ||
| type: 'DataSet', | ||
| label: 'gnomAD v4.1.0', | ||
| version: '4.1.0', | ||
| }, | ||
| focusAlleleCount: 5, | ||
| locusAlleleCount: 100, | ||
| alleleFrequency: 0.05, | ||
| cohort: { id: 'ALL', label: 'Overall', characteristics: null }, | ||
| ancillaryResults: { | ||
| grpMaxFAF95: { frequency: 0.123, confidenceInterval: 0.95, groupId: 'afr' }, | ||
| jointGrpMaxFAF95: { frequency: 0.234, confidenceInterval: 0.95, groupId: 'amr' }, | ||
| homozygotes: 3, | ||
| hemizygotes: 2, | ||
| }, | ||
| subcohortFrequency: [], | ||
| }, | ||
| ] | ||
|
|
||
| expect(resolved).toEqual(expected) | ||
| }) | ||
|
|
||
| test('has the correct subcohortAlleleFrequency when there are multiple CAFs', async () => { | ||
| // Shuffled order of IDs is intentional here to better test sorting | ||
| const subcohortIds = [ | ||
| 'eur_XY', | ||
| 'XY', | ||
| 'ami_XX', | ||
| 'amr', | ||
| 'XX', | ||
| 'ami', | ||
| 'ami_XY', | ||
| 'amr_XX', | ||
| 'eur', | ||
| 'amr_XY', | ||
| 'eur_XX', | ||
| ] | ||
| const subcohortDocuments = subcohortIds.map((subcohortId) => ({ | ||
| ...exomeEsDocument, | ||
| id: subcohortId, | ||
| })) | ||
|
|
||
| const fullDocument = { | ||
| ...variantESDocument, | ||
| exome: { ...exomeEsDocument, ancestry_groups: subcohortDocuments }, | ||
| } | ||
|
|
||
| const resolved = await resolveVACohortAlleleFrequencies(fullDocument, null, null) | ||
| expect(resolved && resolved.length === subcohortIds.length + 1).toEqual(true) | ||
|
|
||
| const subcohortMap: Record<string, string[]> = resolved!.reduce( | ||
| (acc, cohort) => ({ | ||
| ...acc, | ||
| [cohort.id]: cohort.subcohortFrequency.map((subcohort) => subcohort.id), | ||
| }), | ||
| {} | ||
| ) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A']!.sort()).toEqual( | ||
| subcohortIds.map((cohortId) => `gnomad4:1-123-G-A.${cohortId}`).sort() | ||
| ) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A.XX'].sort()).toEqual([ | ||
| 'gnomad4:1-123-G-A.ami_XX', | ||
| 'gnomad4:1-123-G-A.amr_XX', | ||
| 'gnomad4:1-123-G-A.eur_XX', | ||
| ]) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A.XY'].sort()).toEqual([ | ||
| 'gnomad4:1-123-G-A.ami_XY', | ||
| 'gnomad4:1-123-G-A.amr_XY', | ||
| 'gnomad4:1-123-G-A.eur_XY', | ||
| ]) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A.ami'].sort()).toEqual([ | ||
| 'gnomad4:1-123-G-A.ami_XX', | ||
| 'gnomad4:1-123-G-A.ami_XY', | ||
| ]) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A.amr'].sort()).toEqual([ | ||
| 'gnomad4:1-123-G-A.amr_XX', | ||
| 'gnomad4:1-123-G-A.amr_XY', | ||
| ]) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A.eur'].sort()).toEqual([ | ||
| 'gnomad4:1-123-G-A.eur_XX', | ||
| 'gnomad4:1-123-G-A.eur_XY', | ||
| ]) | ||
|
|
||
| expect(subcohortMap['gnomad4:1-123-G-A.ami_XX']).toEqual([]) | ||
| expect(subcohortMap['gnomad4:1-123-G-A.ami_XY']).toEqual([]) | ||
| expect(subcohortMap['gnomad4:1-123-G-A.amr_XX']).toEqual([]) | ||
| expect(subcohortMap['gnomad4:1-123-G-A.amr_XY']).toEqual([]) | ||
| expect(subcohortMap['gnomad4:1-123-G-A.eur_XX']).toEqual([]) | ||
| expect(subcohortMap['gnomad4:1-123-G-A.eur_XY']).toEqual([]) | ||
| }) | ||
| }) |
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