gget
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs. Use when a task needs quick bioinformatics lookup across genomic reference databases with the gget CLI or Python package.
- Kind
- Skill
- Works with
- Claude Code, Codex
- Languages
- Python
- Source
- affaan-m/ECC @ d3b8a3e90890
- Path
- skills/scientific-pkg-gget/SKILL.md
- License
- MIT
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# gget Use this skill when a task needs quick bioinformatics lookup across genomic reference databases with the `gget` CLI or Python package. ## When to Use - Finding Ensembl IDs, gene metadata, transcript details, or sequences. - Running quick BLAST or BLAT lookups without building a full local pipeline. - Fetching reference genome links and annotations from Ensembl. - Querying protein structure, pathway, cancer, expression, or disease-association modules through a single interface. - Creating a reproducible first-pass evidence log before moving to heavier tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific clients. Use a dedicated workflow instead of `gget` when the task requires regulated clinical interpretation, high-throughput production pipelines, or fine-grained control over database versions and local indexes. ## Installation Use a clean Python environment. ```bash python -m venv .venv . .venv/bin/activate python -m pip install --upgrade pip python -m pip install --upgrade gget gget --help ``` If `uv` is available: ```bash uv venv . .venv/bin/activate uv pip install gget ``` …