scientific-pkg-gget

Topics in the source

• gget
• When to Use
• Installation
• Basic Patterns
• Common Modules
• Quick Examples
• Reproducibility Log
• Review Checklist

Use this skill when a task needs quick bioinformatics lookup across genomic reference databases with the gget CLI or Python package. 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. Use a clean Python environment. If uv is available: Before relying on an older environment, upgrade gget and re-check the module docs. The upstream databases queried by gget change over time. CLI shape: Python shape: Common workflow: 1. Identify the species, assembly, gene ID type, and database needed. 2. Check the current module documentation for arguments. 3. Run a small query f

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