API Endpoints Reference¶

This document covers the current HTTP API endpoints for Agentic-SpliceAI services. As the project matures, APIs will grow to cover data preparation, multimodal feature engineering, foundation model inference, and architecture-specific layers.

Splice Analysis Service (port 8004)¶

The splice analysis service provides AI-powered analysis of splice site data.

GET /analyses¶

List available analysis templates.

Response: Array of template objects with name, description, and parameters fields.

POST /analyze/template¶

Generate analysis using a predefined template.

curl -X POST http://localhost:8004/analyze/template \
  -H "Content-Type: application/json" \
  -d '{
    "dataset_path": "data/splice_sites_enhanced.tsv",
    "analysis_type": "high_alternative_splicing",
    "model": "gpt-4o-mini"
  }'

Parameters:

Field	Type	Required	Description
`dataset_path`	string	yes	Path to splice site data file (TSV, CSV, Parquet)
`analysis_type`	string	yes	Template name (e.g., `high_alternative_splicing`, `splice_site_genomic_view`, `exon_complexity`, `strand_bias`, `gene_transcript_diversity`)
`model`	string	no	LLM model to use (default: `gpt-4o-mini`)

POST /analyze/exploratory¶

Generate a custom exploratory analysis from a free-text research question.

curl -X POST http://localhost:8004/analyze/exploratory \
  -H "Content-Type: application/json" \
  -d '{
    "dataset_path": "data/splice_sites_enhanced.tsv",
    "research_question": "What is the relationship between gene length and splice site density?",
    "model": "gpt-4o"
  }'

Parameters:

Field	Type	Required	Description
`dataset_path`	string	yes	Path to splice site data file
`research_question`	string	yes	Free-text research question
`model`	string	no	LLM model to use (default: `gpt-4o-mini`)

Bioinformatics Lab (port 8005)¶

Interactive web UI for gene browsing, splice site visualization, and evaluation metrics.

Gene Browser¶

Method	Endpoint	Description
GET	`/`	Gene Browser page (HTML)
GET	`/api/genes`	List genes with filtering and pagination
GET	`/api/genes/stats`	Summary statistics (gene counts, chromosome distribution)
GET	`/api/genes/chromosomes`	List available chromosomes

/api/genes query parameters: search, chromosome, strand, page, per_page, sort_by, sort_order

Genome View¶

Method	Endpoint	Description
GET	`/genome/{gene}`	Genome View page for a specific gene (HTML)
GET	`/api/genome/{gene}/predict`	Run splice site prediction for a gene

/api/genome/{gene}/predict query parameters:

Parameter	Type	Default	Description
`model`	string	`openspliceai`	Base model (`spliceai` or `openspliceai`)
`threshold`	float	`0.5`	Classification threshold for splice site calls

Metrics Dashboard¶

Method	Endpoint	Description
GET	`/metrics`	Metrics Dashboard page (HTML)
GET	`/api/metrics/runs`	List available evaluation runs
GET	`/api/metrics/{run_id}`	Get detailed metrics for a specific run
GET	`/api/metrics/compare`	Compare metrics across multiple runs

Configuration¶

Environment Variables¶

Variable	Required	Description
`OPENAI_API_KEY`	Yes (for splice service)	OpenAI API key for LLM-powered analysis
`SPLICE_AGENT_PORT`	No	Splice service port (default: 8004)
`SPLICE_AGENT_HOST`	No	Splice service host (default: 0.0.0.0)

Supported LLM Models¶

The splice analysis service supports any OpenAI-compatible model, including: - gpt-4o-mini (default, fast and cost-effective) - gpt-4o (higher quality analysis) - gpt-5-mini (latest generation)

Data Format¶

Required Columns¶

Column	Type	Description
`chrom`	string	Chromosome (e.g., `chr1`, `chrX`)
`position`	int	Genomic position (1-based)
`splice_type`	string	Splice site type (`donor` or `acceptor`)
`strand`	string	Strand (`+` or `-`)

Optional Columns¶

Column	Type	Description
`gene_name`	string	Gene symbol (e.g., `BRCA1`)
`gene_id`	string	Ensembl gene ID (e.g., `ENSG00000012048`)
`transcript_id`	string	Ensembl transcript ID (e.g., `ENST00000357654`)
`exon_rank`	int	Exon number within the transcript

Example TSV Data¶

chrom   position    splice_type strand  gene_name
chr17   43044295    donor   -   BRCA1
chr17   43044294    acceptor    -   BRCA1
chr17   43045802    donor   -   BRCA1

See also: docs/system_design/configuration_system.md for Pydantic-based configuration patterns