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.
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:
uv venv
. .venv/bin/activate
uv pip install gget
Before relying on an older environment, upgrade gget and re…
