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Update Genome Nexus api clients to include new Mutation Assessor
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@leexgh
leexgh committed Sep 30, 2024
1 parent 1dd45af commit a076bf2
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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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