A specialized tool for generating high-fidelity genomic visualizations of gene structures, including exons, introns, domains, and mutation hotspots.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install gene-structure-mapper
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install gene-structure-mapper using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is Gene Structure Mapper?
Gene Structure Mapper is a robust Openclaw Skills utility designed for bioinformaticians and researchers who need to transform genomic data into publication-ready visual assets. By interfacing directly with the Ensembl REST API, it automates the retrieval of exon-intron coordinates and provides a scalable way to visualize gene architecture.
Beyond basic mapping, the tool integrates UniProt protein domain annotations and custom mutation markers, allowing users to create high-context diagrams in SVG, PNG, or PDF formats. Whether you are analyzing splice variants or preparing figures for a manuscript, this skill provides a programmatic and reproducible workflow for genomic visualization.
Gene Structure Mapper Use Cases
- Creating gene structure figures for academic manuscripts or scientific presentations.
- Visualizing differences in splice variants and transcript isoforms.
- Mapping specific mutation hotspot positions onto physical gene diagrams for functional impact studies.
- Overlaying protein domain boundaries directly onto genomic exon-intron maps.
How Gene Structure Mapper Works
- The user provides a gene symbol or Ensembl ID along with desired visualization parameters.
- The skill queries the Ensembl REST API to retrieve precise genomic coordinates for exons and introns.
- If requested, it fetches protein domain data from UniProt and maps amino acid positions to genomic coordinates.
- Mutation positions are validated and translated into markers on the specific codon locations.
- The tool utilizes matplotlib to render a scaled diagram and saves the output in the specified vector or raster format.
Gene Structure Mapper Setup
To use this Openclaw Skills tool, ensure you have Python installed and can run the following commands:
# Verify the script compilation
python -m py_compile scripts/main.py
# View all available parameters and help
python scripts/main.py --help
# Run a test generation using the built-in demo data
python scripts/main.py --demo --output demo.png
Gene Structure Mapper Data Schema & Taxonomy
The skill organizes data through a combination of API fetching and local caching to ensure performance and rate-limit compliance.
| Data Type | Source/Storage | Format |
|---|---|---|
| Genomic Coordinates | Ensembl REST API | JSON |
| Domain Annotations | UniProt API | JSON |
| Local Cache | .cache/{gene}_ensembl.json |
JSON |
| Output Figures | Local Directory | SVG, PNG, PDF |
Gene Structure Mapper Advanced Features
- Smart Caching: Automatically stores Ensembl API responses locally to prevent redundant network calls and avoid rate-limiting.
- Domain Annotation Overlay: Automatically maps UniProt protein domains onto the genomic structure using the
--domainsflag. - Mutation Mapping: Supports precise vertical markers for codon positions via the
--mutationsparameter. - Multi-Format Export: Supports lossless vector formats (SVG, PDF) for high-resolution publication requirements.
- Offline Demo Mode: Includes hardcoded GRCh38 data for TP53 to allow for immediate testing without internet access.
SKILL.md
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