/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, 300–500,000 bp (whitespace stripped). 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 of 300–500,000 bp, 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`. 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 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`. Omit `model` and the API resolves the default — a GENA-LM BERT Large transformer with a 2000 bp context and a 1000 bp prediction window. Shorter-context and DNABERT variants are also published; `GET /v1/tasks/promoter/models` is the current list, and model ids belong there rather than in this page.

> **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**: read single-record FASTA via the shared `clawbio.gi.gi_client.read_fasta` helper (uppercase; refuses multi-record input and any base outside `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

# Pick a specific model (ids come from GET /v1/tasks/promoter/models)
python skills/gi-promoter/gi_promoter.py --demo --model <model-id>

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

Demo

python clawbio.py run gi-promoter --demo

Bundled fixture is the TP53 locus (25.8 kbp, GRCh38, gene-sense). Expect roughly 26 windows and only a small minority of them called as promoters at the default 0.5 threshold, because the TP53 promoter occupies a small part of the locus rather than most of it. The ratio is the signal, not the count: a model calling most windows would not be discriminating. Read the counts from your own run.

Authentication

The skill requires a