UCSC Genome Browser REST API — Sequences

naftiko: 1.0.0-alpha2
info:
  label: UCSC Genome Browser REST API — Sequences
  description: 'UCSC Genome Browser REST API — Sequences. 1 operations. Lead operation: Get DNA Sequence. Self-contained Naftiko
    capability covering one Ucsc Genomic Data business surface.'
  tags:
  - Ucsc Genomic Data
  - Sequences
  created: '2026-05-19'
  modified: '2026-05-19'
binds:
- namespace: env
  keys:
    UCSC_GENOMIC_DATA_API_KEY: UCSC_GENOMIC_DATA_API_KEY
capability:
  consumes:
  - type: http
    namespace: ucsc-genomic-data-sequences
    baseUri: https://api.genome.ucsc.edu
    description: UCSC Genome Browser REST API — Sequences business capability. Self-contained, no shared references.
    resources:
    - name: getData-sequence
      path: /getData/sequence
      operations:
      - name: getdnasequence
        method: GET
        description: Get DNA Sequence
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: genome
          in: query
          type: string
          description: Genome assembly identifier (e.g., hg38, mm39).
          required: true
        - name: chrom
          in: query
          type: string
          description: Chromosome identifier (e.g., chr1, chrM).
          required: true
        - name: start
          in: query
          type: integer
          description: Start position (0-based, half-open coordinates).
        - name: end
          in: query
          type: integer
          description: End position (1-based, half-open coordinates).
        - name: revComp
          in: query
          type: integer
          description: Set to 1 to return the reverse complement sequence.
        - name: hubUrl
          in: query
          type: string
          description: URL of the hub.txt file for a sequence hub.
  exposes:
  - type: rest
    namespace: ucsc-genomic-data-sequences-rest
    port: 8080
    description: REST adapter for UCSC Genome Browser REST API — Sequences. One Spectral-compliant resource per consumed operation,
      prefixed with /v1.
    resources:
    - path: /v1/getdata/sequence
      name: getdata-sequence
      description: REST surface for getData-sequence.
      operations:
      - method: GET
        name: getdnasequence
        description: Get DNA Sequence
        call: ucsc-genomic-data-sequences.getdnasequence
        with:
          genome: rest.genome
          chrom: rest.chrom
          start: rest.start
          end: rest.end
          revComp: rest.revComp
          hubUrl: rest.hubUrl
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: ucsc-genomic-data-sequences-mcp
    port: 9090
    transport: http
    description: MCP adapter for UCSC Genome Browser REST API — Sequences. One tool per consumed operation, routed inline
      through this capability's consumes block.
    tools:
    - name: get-dna-sequence
      description: Get DNA Sequence
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ucsc-genomic-data-sequences.getdnasequence
      with:
        genome: tools.genome
        chrom: tools.chrom
        start: tools.start
        end: tools.end
        revComp: tools.revComp
        hubUrl: tools.hubUrl
      outputParameters:
      - type: object
        mapping: $.