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.
version	0.1.0
author	ClawBio + Genomic Intelligence
domain	genomics
license	MIT
tags	["genomics","splice","splice-site","splicing","intron-exon","dna-lm","transformer","gi-api"]
inputs	[{"name":"input_file","type":"file","format":["fa","fasta","fna"],"description":"Single-record FASTA, 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 (position, kind, strand, probability)."},{"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."}]
dependencies	{"python":">=3.10","packages":["requests>=2.31"]}
demo_data	[{"path":"example_data/splice_hbb.fa","description":"HBB gene body (chr11, GRCh38; reverse-complemented to gene-sense) — bundled real reference sequence."}]
endpoints	{"cli":"python skills/gi-splice/gi_splice.py --input {input_file} --output {output_dir}"}
metadata	{"openclaw":{"requires":{"bins":["python3"],"env":[],"config":[]},"always":false,"emoji":"✂️","homepage":"https://docs.genomicintelligence.ai","os":["darwin","linux"],"install":[{"kind":"pip","package":"requests","bins":[]}],"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"]}}

✂️ 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 skill refuses to run unless GI_API_KEY is set — cp .env.example .env && set -a && source .env && set +a to use the shared ClawBio hackathon key (50 concurrent / 120 rpm), or request an individual key at [e-mail]. Prefer a browser? The same models run interactively at https://genomicintelligence.ai. Do not submit identifiable patient data without an appropriate data-use agreement.

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 — default model g0-splice-bigbird (G0 BigBird transformer; long-context handling for full gene bodies).

Workflow

1. Parse: single-record FASTA via clawbio.gi.gi_client.read_fasta.
2. Authenticate: --api-key → GI_API_KEY → bundled hackathon key.
3. POST the full gene body to /v1/tasks/splice/predict.
4. 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 ~8 sites (≈4 donor + 4 acceptor, including lower-confidence alternates).

Authentication

Same as other gi-* skills: GI_API_KEY env overrides the bundled hackathon key.

Gotchas

• Submit gene-sense, not genomic-sense. Minus-strand genes need RC'd input. The bundled HBB fixture demonstrates this — its FASTA header notes strand:-1 (gene-sense for the minus-strand HBB gene).
• Full gene body, not just an exon. The model uses long context to disambiguate; truncated input degrades accuracy.
• Donor/acceptor pairs. The model emits independent site calls. Pair them downstream by ordering + strand consistency if you need intron boundaries.
• Hackathon key is shared — GI_API_KEY for serious work.

Output Structure

output_dir/
├── report.md              # Site table (position, kind, strand, probability)
├── result.json            # Full {data, meta} envelope
└── reproducibility/
    ├── command.sh
    └── environment.json

Integration with Bio Orchestrator

Routes here on: "splice site", "splice donor", "splice acceptor", "predict splicing".

Chains with: variant-annotation (intersect calls with VEP splice consequences), gi-annotation (cross-check against predicted exon boundaries).

Safety

Research tool. Not a clinical assay.