/gi-splice

name: gi-splice
description: Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities
  and called sites.
license: MIT
metadata:
  openclaw:
    requires:
      bins:
      - python3
      env: null
      config: null
    always: false
    emoji: ✂️
    homepage: https://docs.genomicintelligence.ai
    os:
    - darwin
    - linux
    install:
    - kind: pip
      package: requests
      bins: null
    trigger_keywords:
    - splice
    - splice site
    - splice donor
    - splice acceptor
    - splicing prediction
    - intron exon boundary
    - cryptic splice site
    - GT-AG site
    - gi splice
    - G0 splice
    - genomic intelligence splice
  author: ClawBio + Genomic Intelligence
  demo_data:
  - path: example_data/splice_hbb.fa
    description: HBB gene body (chr11, GRCh38; reverse-complemented to gene-sense) — bundled real reference sequence.
  dependencies:
    python: '>=3.10'
    packages:
    - requests>=2.31
  domain: genomics
  endpoints:
    cli: python skills/gi-splice/gi_splice.py --input {input_file} --output {output_dir}
  inputs:
  - name: input_file
    type: file
    format:
    - fa
    - fasta
    - fna
    description: Single-record FASTA, 100–500,000 bp (whitespace stripped), typically a gene body (5'UTR → 3'UTR including introns).
    required: false
  outputs:
  - name: report
    type: file
    format: md
    description: Markdown report — sequence + model metadata, called splice sites (name, span, type, strand, score).
  - name: result
    type: file
    format: json
    description: Full `{data, meta}` response from the GI API plus a flattened summary.
  - name: reproducibility
    type: directory
    description: command.sh + environment.json for exact-rerun reproducibility.
  tags:
  - genomics
  - splice
  - splice-site
  - splicing
  - intron-exon
  - dna-lm
  - transformer
  - gi-api
  version: 0.1.0

✂️ gi-splice

You are **gi-splice**, a ClawBio agent that calls the **Genomic Intelligence** splice-site model. Given a gene-body sequence, it returns called donor/acceptor sites and per-position probabilities via the hosted API.

> ⚠️ **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https://genomicintelligence.ai>. **Do not submit identifiable patient data** without an appropriate data-use agreement. Key setup: see [Authentication](#authentication) below.

Trigger

**Fire this skill when the user says any of:**

• "predict splice sites in this gene"
• "find splice donors/acceptors"
• "score this for cryptic splice sites"
• "splice site prediction"
• "gi-splice", "G0 splice"
• "where does this transcript splice?"

**Do NOT fire when:**

• The user asks for full transcript structure (multi-exon annotation) → `gi-annotation`
• The user asks about variant effect on splicing → use `variant-annotation` (VEP) or chain `gi-splice` ref/alt comparisons

Why This Exists

• **Without it**: SpliceAI / similar require local GPU + weights + careful preprocessing.
• **With it**: One CLI call → ranked site list with positions and probabilities, in ~1 s.
• **Why ClawBio**: Hosted G0 BigBird inference plus ClawBio's reproducibility bundle and chaining (`gi-splice` → `gi-annotation` → variant interpretation).

API Backed

`POST https://api.genomicintelligence.ai/v1/tasks/splice/predict`. Omit `model` and the API resolves the default — a BigBird transformer whose long context handles full gene bodies. `GET /v1/tasks/splice/models` is the current list.

> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 validation_failed`, not a silent ignore). The bounds quoted in this file are the published ones, but the authority is always the served schema: `GET https://api.genomicintelligence.ai/v1/openapi.json`.

Workflow

1. **Parse**: single-record FASTA via `clawbio.gi.gi_client.read_fasta`. 2. **POST** the full gene body to `/v1/tasks/splice/predict`. 3. **Render**: `report.md` + `result.json` + `reproducibility/`.

CLI Reference

# Demo — bundled HBB gene body
python skills/gi-splice/gi_splice.py --demo --output /tmp/gi-splice-demo

# Your own FASTA
python skills/gi-splice/gi_splice.py --input my_gene.fa --output report_dir

# Via ClawBio runner
python clawbio.py run gi-splice --demo

Demo

python clawbio.py run gi-splice --demo

Bundled fixture is HBB (β-globin) gene body, reverse-complemented to gene-sense. HBB has 3 exons / 2 introns; on the coding strand the model calls donor and acceptor sites at the annotated intron boundaries, plus lower-confidence alternates. Read the counts and scores from your own run.

Authentication

The skill requires a Genomic Intelligence partner key in `GI_API_KEY`. Resolution order:

1. `--api-key <value>` CLI flag (explicit override). 2. `GI_API_KEY` environment variable. 3. Otherwise: the skill raises a `RuntimeError` pointing here.

Quick start — ClawBio hackathon key

A shared hackathon-tier key ships in `.env.example` at the repo root (opt-in only). Caps are per-key and are not published as a fixed number — read `RateLimit-Limit` / `RateLimit-Remaining` on any `/v1/tasks/` response for the live allowance. The runner keeps them for you: they are in `result.json` under `rate_limit`, and a `429` names them on the error line. From wherever the ClawBio files live on your machine:

# Repo root (git clone) — or ~/.claude/plugins/cache/clawbio/clawbio/<version>/ for plugin installs
cp .env.example .env
set -a && source .env && set +a

Production / heavier use

Request an individu