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API client update about Mutation Assessor v4 data and UI changes #5015

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API client update about Mutation Assessor v4 data and UI changes #5015

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a076bf2
Update Genome Nexus api clients to include new Mutation Assessor
leexgh Sep 30, 2024
8ab1fcb
Changes to fit new Mutation Assessor data model
leexgh Oct 2, 2024
6cdc6a3
Add note on tooltip to indicate this is v4 data
leexgh Oct 3, 2024
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140 changes: 37 additions & 103 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2506,6 +2506,26 @@
}
}
},
"IntergenicConsequenceSummary": {
"type": "object",
"properties": {
"consequenceTerms": {
"type": "array",
"items": {
"type": "string"
}
},
"impact": {
"type": "string"
},
"variantAllele": {
"type": "string"
},
"variantClassification": {
"type": "string"
}
}
},
"IntergenicConsequences": {
"type": "object",
"required": [
Expand Down Expand Up @@ -2554,124 +2574,32 @@
},
"MutationAssessor": {
"type": "object",
"required": [
"input"
],
"properties": {
"codonStartPosition": {
"type": "string",
"description": "Codon start position"
},
"cosmicCount": {
"type": "integer",
"format": "int32",
"description": "Number of mutations in COSMIC for this protein"
},
"functionalImpact": {
"type": "string",
"description": "Functional impact"
"functionalImpactPrediction": {
"type": "string"
},
"functionalImpactScore": {
"type": "number",
"format": "double",
"description": "Functional impact score"
},
"hgvs": {
"hgvspShort": {
"type": "string"
},
"hugoSymbol": {
"type": "string",
"description": "Hugo gene symbol"
},
"input": {
"type": "string",
"description": "User-input variants"
},
"mappingIssue": {
"type": "string",
"description": "Mapping issue info"
},
"msaGaps": {
"type": "number",
"format": "double",
"description": "Portion of gaps in variant position in multiple sequence alignment"
},
"msaHeight": {
"mav": {
"type": "integer",
"format": "int32",
"description": "Number of diverse sequences in multiple sequence alignment (identical or highly similar sequences filtered out)"
},
"msaLink": {
"type": "string",
"description": "Link to multiple sequence alignment"
},
"pdbLink": {
"type": "string",
"description": "Link to 3d structure browser"
},
"referenceGenomeVariant": {
"type": "string",
"description": "Reference genome variant"
},
"referenceGenomeVariantType": {
"type": "string",
"description": "Reference genome variant type"
},
"refseqId": {
"type": "string",
"description": "Refseq protein ID"
},
"refseqPosition": {
"type": "integer",
"format": "int32",
"description": "Variant position in Refseq protein, can be different from the one in Uniprot"
"format": "int32"
},
"refseqResidue": {
"type": "string",
"description": "Reference residue in Refseq protein, can be different from the one in Uniprot"
"msa": {
"type": "string"
},
"snpCount": {
"sv": {
"type": "integer",
"format": "int32",
"description": "Number of SNPs in dbSNP for this protein"
"format": "int32"
},
"uniprotId": {
"type": "string",
"description": "Uniprot protein accession ID"
},
"uniprotPosition": {
"type": "integer",
"format": "int32",
"description": "Variant position in Uniprot protein, can be different from the one in Refseq"
},
"uniprotResidue": {
"type": "string",
"description": "Reference residue in Uniprot protein, can be different from the one in Refseq"
},
"variant": {
"type": "string",
"description": "Amino acid substitution"
},
"variantConservationScore": {
"type": "number",
"format": "double",
"description": "Variant conservation score"
},
"variantSpecificityScore": {
"type": "number",
"format": "double",
"description": "Variant specificity score"
}
}
},
"MutationAssessorAnnotation": {
"type": "object",
"properties": {
"annotation": {
"$ref": "#/definitions/MutationAssessor"
},
"license": {
"type": "string"
}
}
},
Expand Down Expand Up @@ -3676,8 +3604,8 @@
"description": "Most severe consequence"
},
"mutation_assessor": {
"description": "Mutation Assessor Annotation",
"$ref": "#/definitions/MutationAssessorAnnotation"
"description": "Mutation Assessor",
"$ref": "#/definitions/MutationAssessor"
},
"my_variant_info": {
"description": "My Variant Info Annotation",
Expand Down Expand Up @@ -3758,6 +3686,12 @@
"description": "Genomic location",
"$ref": "#/definitions/GenomicLocation"
},
"intergenicConsequenceSummaries": {
"type": "array",
"items": {
"$ref": "#/definitions/IntergenicConsequenceSummary"
}
},
"strandSign": {
"type": "string",
"description": "Strand (- or +)"
Expand Down
64 changes: 18 additions & 46 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -483,6 +483,16 @@ export type IntegerRange = {

'start': number

};
export type IntergenicConsequenceSummary = {
'consequenceTerms': Array < string >

'impact': string

'variantAllele': string

'variantClassification': string

};
export type IntergenicConsequences = {
'impact': string
Expand All @@ -501,60 +511,20 @@ export type MainType = {

};
export type MutationAssessor = {
'codonStartPosition': string

'cosmicCount': number

'functionalImpact': string
'functionalImpactPrediction': string

'functionalImpactScore': number

'hgvs': string

'hugoSymbol': string

'input': string

'mappingIssue': string

'msaGaps': number

'msaHeight': number

'msaLink': string

'pdbLink': string

'referenceGenomeVariant': string

'referenceGenomeVariantType': string

'refseqId': string
'hgvspShort': string

'refseqPosition': number
'mav': number

'refseqResidue': string
'msa': string

'snpCount': number
'sv': number

'uniprotId': string

'uniprotPosition': number

'uniprotResidue': string

'variant': string

'variantConservationScore': number

'variantSpecificityScore': number

};
export type MutationAssessorAnnotation = {
'annotation': MutationAssessor

'license': string

};
export type MutationEffectResp = {
'citations': Citations
Expand Down Expand Up @@ -1008,7 +978,7 @@ export type VariantAnnotation = {

'most_severe_consequence': string

'mutation_assessor': MutationAssessorAnnotation
'mutation_assessor': MutationAssessor

'my_variant_info': MyVariantInfoAnnotation

Expand Down Expand Up @@ -1044,6 +1014,8 @@ export type VariantAnnotationSummary = {

'genomicLocation': GenomicLocation

'intergenicConsequenceSummaries': Array < IntergenicConsequenceSummary >

'strandSign': string

'transcriptConsequenceSummaries': Array < TranscriptConsequenceSummary >
Expand Down
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