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, 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."}],"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. 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 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 — 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. POST the full gene body to /v1/tasks/splice/predict.
3. Render: report.md + result.json + reproducibility/.