/gi-promoter

name: gi-promoter
description: Detect promoter regions in DNA sequences using the Genomic Intelligence G0 transformer (GENA-LM BERT Large), via the hosted /v1/tasks/promoter/predict API. Returns per-window promoter probabilities
  and called regions.
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:
    - promoter
    - promoter prediction
    - predict promoter
    - find promoter
    - promoter region
    - TSS prediction
    - transcription start site
    - gi promoter
    - genomic intelligence promoter
    - G0 promoter
    - GENA-LM promoter
  author: ClawBio + Genomic Intelligence
  demo_data:
  - path: example_data/promoter_tp53.fa
    description: TP53 locus, gene-sense (chr17:7661779-7687546, GRCh38, 25.8 kbp; TP53 is minus-strand, so this is the reverse complement) — bundled real reference sequence.
  dependencies:
    python: '>=3.10'
    packages:
    - requests>=2.31
  domain: genomics
  endpoints:
    cli: python skills/gi-promoter/gi_promoter.py --input {input_file} --output {output_dir}
  inputs:
  - name: input_file
    type: file
    format:
    - fa
    - fasta
    - fna
    description: Single-record FASTA. Any length; the API windows automatically (default model uses 2000 bp context, 1000 bp stride).
    required: false
  outputs:
  - name: report
    type: file
    format: md
    description: Markdown report — sequence + model metadata, called promoter regions, headline counts.
  - 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
  - promoter
  - transcription
  - regulatory
  - dna-lm
  - transformer
  - gi-api
  version: 0.1.0

🧬 gi-promoter

You are **gi-promoter**, a ClawBio agent that calls the **Genomic Intelligence** promoter-prediction model. Given a DNA sequence (any length), it returns per-window promoter probabilities and called regions, all in a few hundred milliseconds 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`. Prefer a browser? The same models 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 promoters in this sequence"
• "find promoters in [gene/region]"
• "is this a promoter?"
• "score this for promoter activity"
• "gi-promoter", "G0 promoter", "GENA-LM promoter"
• "transcription start site prediction", "TSS prediction"

**Do NOT fire when:**

• The user asks for splice sites → `gi-splice`
• The user asks for enhancer activity → `gi-enhancer`
• The user asks for chromatin state → `gi-chromatin`
• The user asks for gene/transcript structure → `gi-annotation`

Why This Exists

• **Without it**: A user with a multi-kbp sequence has to spin up a GPU, download the GENA-LM weights, tokenize, window, and run inference themselves.
• **With it**: One CLI call → annotated report in <1 s for typical sequences. The model is hosted; see [Authentication](#authentication) for key setup.
• **Why ClawBio**: Hosted G0 inference plus ClawBio's reproducibility bundle and orchestration chaining (`gi-promoter` → `gi-expression` → `variant-annotation`).

API Backed

`POST https://api.genomicintelligence.ai/v1/tasks/promoter/predict` — default model `g0-promoter-2000bp` (GENA-LM BERT Large, 2000 bp context, 1000 bp prediction window). Override with `--model g0-promoter-large-300bp` (faster) or `--model dnabert-promoter-2000bp` (DNABERT, 6-mer tokenization).

Workflow

1. **Parse**: read single-record FASTA via the shared `clawbio.gi.gi_client.read_fasta` helper (uppercase, strip non-ACGTN). 2. **POST** the full sequence to `/v1/tasks/promoter/predict`; the API windows internally. 3. **Render**: write `report.md` (summary + region table), `result.json` (full `{data, meta}` envelope), `reproducibility/`.

CLI Reference

# Demo — bundled TP53 region
python skills/gi-promoter/gi_promoter.py --demo --output /tmp/gi-promoter-demo

# Your own FASTA
python skills/gi-promoter/gi_promoter.py --input my_region.fa --output report_dir

# Faster 300-bp model
python skills/gi-promoter/gi_promoter.py --demo --model g0-promoter-large-300bp

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

Demo

python clawbio.py run gi-promoter --demo

Bundled fixture is the TP53 locus (19 kbp, GRCh38). Expect ~20 windows, near-zero promoter calls at the default 0.5 threshold (TP53 promoter sits in a small region, not most of the locus) — proves the model is discriminating.

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 (50 concurrent / 120 rpm, opt-in only). 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 individual key at **contact@genomicintelligence.ai**, then:

export GI_API_KEY=gi_yourkeyhere

Gotchas

• **Don't pre-wind