Gi Promoter

🧬 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 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 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 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 individual key at contact@genomicintelligence.ai, then:

export GI_API_KEY=gi_yourkeyhere