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feat: adding store/geneInfo #72

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Feb 1, 2024
Merged

feat: adding store/geneInfo #72

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11 changes: 11 additions & 0 deletions src/api/annonars/__snapshots__/client.spec.ts.snap
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32 changes: 11 additions & 21 deletions src/api/annonars/client.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,7 @@ import createFetchMock from 'vitest-fetch-mock'
import { LinearStrucvarImpl, SeqvarImpl } from '../../lib/genomicVars'
import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
import { AnnonarsClient } from './client'
import {
ClinvarSvQueryResponse,
GeneInfoResult,
GeneSearchResponse,
SeqvarInfoResponse
} from './types'
import { ClinvarSvQueryResponse } from './types'

const geneInfoBrca1Json = JSON.parse(
fs.readFileSync(
Expand All @@ -28,6 +23,9 @@ const searchInfoInfoEmpJson = JSON.parse(
const clinvarStrucvarResponseBrca1Json = JSON.parse(
fs.readFileSync(path.resolve(__dirname, './fixture.strucvarClinvarResponse.BRCA1.json'), 'utf8')
)
const clinvarPerGeneInfoResponseBrca1Json = JSON.parse(
fs.readFileSync(path.resolve(__dirname, './fixture.geneClinvar.BRCA1.json'), 'utf8')
)

const fetchMocker = createFetchMock(vi)

Expand All @@ -49,9 +47,7 @@ describe.concurrent('AnnonarsClient.fetchGeneInfo()', () => {
const result = await client.fetchGeneInfo('BRCA1')

// assert:
expect(JSON.stringify(result)).toEqual(
JSON.stringify(GeneInfoResult.fromJson({ genes: { 'HGNC:1100': geneInfoBrca1Json } }))
)
expect(JSON.stringify(result)).toMatchSnapshot()
})

it('fails to fetch gene info with wrong HGNC id', async () => {
Expand Down Expand Up @@ -89,9 +85,7 @@ describe.concurrent('AnnonarsClient.fetchVariantInfo()', () => {
const result = await client.fetchVariantInfo(seqvar)

// assert:
expect(JSON.stringify(result)).toEqual(
JSON.stringify(SeqvarInfoResponse.fromJson(variantInfoBrca1Json))
)
expect(JSON.stringify(result)).toMatchSnapshot()
})

it('do removes chr prefix from chromosome if genome release is grch38', async () => {
Expand All @@ -108,9 +102,7 @@ describe.concurrent('AnnonarsClient.fetchVariantInfo()', () => {
const result = await client.fetchVariantInfo(seqvar)

// assert:
expect(JSON.stringify(result)).toEqual(
JSON.stringify(SeqvarInfoResponse.fromJson(variantInfoBrca1Json))
)
expect(JSON.stringify(result)).toMatchSnapshot()
})

it('fails to fetch variant info with wrong variant', async () => {
Expand Down Expand Up @@ -142,14 +134,14 @@ describe.concurrent('AnnonarsClient.fetchGeneClinvarInfo()', () => {

it('fetches gene clinvar info correctly', async () => {
// arrange:
fetchMocker.mockResponseOnce(JSON.stringify(geneInfoBrca1Json))
fetchMocker.mockResponseOnce(JSON.stringify(clinvarPerGeneInfoResponseBrca1Json))

// act:
const client = new AnnonarsClient()
const result = await client.fetchGeneClinvarInfo('BRCA1')
const result = await client.fetchGeneClinvarInfo('HGNC:1100')

// assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(geneInfoBrca1Json))
expect(JSON.stringify(result)).toMatchSnapshot()
})

it('fails to fetch gene clinvar info with wrong HGNC id', async () => {
Expand Down Expand Up @@ -190,9 +182,7 @@ describe.concurrent('AnnonarsClient.fetchGenes()', () => {
)

// assert:
expect(JSON.stringify(result)).toEqual(
JSON.stringify(GeneSearchResponse.fromJson(searchInfoInfoEmpJson))
)
expect(JSON.stringify(result)).toMatchSnapshot()
})

it('fails to fetch genes with wrong query', async () => {
Expand Down
7 changes: 6 additions & 1 deletion src/api/annonars/client.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,12 @@ export class AnnonarsClient {
if (!response.ok) {
throw new Error(`failed to fetch gene clinvar info: ${response.statusText}`)
}
return await response.json()
const responseJson = await response.json()
if (responseJson?.genes && responseJson?.genes[hgncId]) {
return ClinvarPerGeneRecord.fromJson(responseJson.genes[hgncId])
} else {
throw new Error(`failed to fetch gene clinvar info for HGNC ID: ${hgncId}`)
}
}

/**
Expand Down
216 changes: 216 additions & 0 deletions src/api/annonars/fixture.geneClinvar.BRCA1.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,216 @@
{
"genes": {
"HGNC:1100": {
"perImpactCounts": [
{ "impact": "IMPACT_THREE_PRIME_UTR_VARIANT", "counts": [30, 112, 196, 41, 115] },
{ "impact": "IMPACT_FIVE_PRIME_UTR_VARIANT", "counts": [47, 376, 244, 33, 275] },
{ "impact": "IMPACT_FRAMESHIFT_VARIANT", "counts": [0, 1, 31, 115, 3883] },
{ "impact": "IMPACT_INFRAME_INDEL", "counts": [5, 15, 168, 10, 20] },
{ "impact": "IMPACT_INTRON_VARIANT", "counts": [1085, 4679, 3585, 186, 1701] },
{ "impact": "IMPACT_MISSENSE_VARIANT", "counts": [124, 374, 2202, 158, 212] },
{ "impact": "IMPACT_NON_CODING_TRANSCRIPT_VARIANT", "counts": [0, 1, 7, 9, 437] },
{ "impact": "IMPACT_STOP_GAINED", "counts": [1, 0, 1, 1, 12] },
{ "impact": "IMPACT_SPLICE_ACCEPTOR_VARIANT", "counts": [0, 1, 4, 13, 82] },
{ "impact": "IMPACT_SPLICE_DONOR_VARIANT", "counts": [0, 0, 7, 10, 87] },
{ "impact": "IMPACT_SYNONYMOUS_VARIANT", "counts": [11, 178, 7, 0, 5] },
{ "impact": "IMPACT_UPSTREAM_TRANSCRIPT_VARIANT", "counts": [4, 0, 0, 0, 0] }
],
"perFreqCounts": [
{
"coarseClinsig": "COARSE_CLINICAL_SIGNIFICANCE_BENIGN",
"counts": [5712, 0, 0, 0, 0, 317, 87, 101, 133, 133, 113, 122, 31, 18, 24, 279, 3, 0]
},
{
"coarseClinsig": "COARSE_CLINICAL_SIGNIFICANCE_UNCERTAIN",
"counts": [6318, 0, 0, 0, 0, 173, 22, 20, 3, 2, 4, 3, 0, 1, 0, 10, 0, 0]
},
{
"coarseClinsig": "COARSE_CLINICAL_SIGNIFICANCE_PATHOGENIC",
"counts": [7934, 0, 0, 0, 0, 35, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
}
],
"variants": [
{
"genomeRelease": "GRCh37",
"variants": [
{
"release": "GRCh37",
"chromosome": "17",
"start": 41197708,
"stop": 41197708,
"reference": "T",
"alternative": "G",
"vcv": "VCV000041833",
"referenceAssertions": [
{
"rcv": "RCV000034760",
"title": "NM_007294.4(BRCA1):c.5579A>C (p.His1860Pro) AND not provided",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_BENIGN",
"reviewStatus": "REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED"
}
]
},
{
"release": "GRCh37",
"chromosome": "17",
"start": 41234473,
"stop": 41234473,
"reference": "G",
"alternative": "C",
"vcv": "VCV000182080",
"referenceAssertions": [
{
"rcv": "RCV000159851",
"title": "NM_007294.4(BRCA1):c.4305C>G (p.Asp1435Glu) AND not provided",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
},
{
"release": "GRCh37",
"chromosome": "17",
"start": 41234589,
"stop": 41234591,
"reference": "CTCT",
"alternative": "C",
"vcv": "VCV000182116",
"referenceAssertions": [
{
"rcv": "RCV000159925",
"title": "NM_007294.4(BRCA1):c.4187_4189del (p.Gln1396del) AND not provided",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
},
{
"release": "GRCh37",
"chromosome": "17",
"start": 41226408,
"stop": 41226409,
"reference": "GC",
"alternative": "AA",
"vcv": "VCV000182117",
"referenceAssertions": [
{
"rcv": "RCV000159926",
"title": "NM_007294.4(BRCA1):c.4614_4615delinsTT (p.Gln1538His) AND not specified",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
},
{
"release": "GRCh37",
"chromosome": "17",
"start": 41276145,
"stop": 41276149,
"reference": "AGAAA",
"alternative": "TT",
"vcv": "VCV000246265",
"referenceAssertions": [
{
"rcv": "RCV000235381",
"title": "NM_007294.4(BRCA1):c.-19-17_-19-13delinsAA AND not specified",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
}
]
},
{
"genomeRelease": "GRCh38",
"variants": [
{
"release": "GRCh38",
"chromosome": "17",
"start": 43045691,
"stop": 43045691,
"reference": "T",
"alternative": "G",
"vcv": "VCV000041833",
"referenceAssertions": [
{
"rcv": "RCV000034760",
"title": "NM_007294.4(BRCA1):c.5579A>C (p.His1860Pro) AND not provided",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_BENIGN",
"reviewStatus": "REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED"
}
]
},
{
"release": "GRCh38",
"chromosome": "17",
"start": 43082456,
"stop": 43082456,
"reference": "G",
"alternative": "C",
"vcv": "VCV000182080",
"referenceAssertions": [
{
"rcv": "RCV000159851",
"title": "NM_007294.4(BRCA1):c.4305C>G (p.Asp1435Glu) AND not provided",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
},
{
"release": "GRCh38",
"chromosome": "17",
"start": 43082572,
"stop": 43082574,
"reference": "CTCT",
"alternative": "C",
"vcv": "VCV000182116",
"referenceAssertions": [
{
"rcv": "RCV000159925",
"title": "NM_007294.4(BRCA1):c.4187_4189del (p.Gln1396del) AND not provided",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
},
{
"release": "GRCh38",
"chromosome": "17",
"start": 43074391,
"stop": 43074392,
"reference": "GC",
"alternative": "AA",
"vcv": "VCV000182117",
"referenceAssertions": [
{
"rcv": "RCV000159926",
"title": "NM_007294.4(BRCA1):c.4614_4615delinsTT (p.Gln1538His) AND not specified",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
},
{
"release": "GRCh38",
"chromosome": "17",
"start": 43124128,
"stop": 43124132,
"reference": "AGAAA",
"alternative": "TT",
"vcv": "VCV000246265",
"referenceAssertions": [
{
"rcv": "RCV000235381",
"title": "NM_007294.4(BRCA1):c.-19-17_-19-13delinsAA AND not specified",
"clinicalSignificance": "CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE",
"reviewStatus": "REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"
}
]
}
]
}
]
}
}
}
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