Agent skill · research science · affaan-m
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.
Why this skill is useful
Provides specific commands and workflows for genomic database queries that the AI wouldn't reliably generate on its own.
What it needs
Requires python installed locally. About 3k tokens when loaded. Last updated 2026-08-06. 238,342 stars on the source repository.
What this skill does
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. 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. Basic Patterns 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 first. 4. Save output with an explicit filename and date. 5. Record module name, version, arguments, and database assumptions. Common Modules Use current upstream docs for exact arguments. These modules are common first choices: gget search: find Ensembl IDs from search terms. gget info: retrieve metadata for Ensembl, UniProt, or related IDs. gget seq: fetch nucleotide or amino-acid sequences. gget ref: retrieve reference genome download links. gget blast: run a quick BLAST query. gget blat: locate a sequence against supported genome assemblies. gget muscle: run multiple sequence alignment. gget diamond: run local sequence alignment against reference sequences. gget alphafold and gget pdb: inspect protein-structure references. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills affaan-m/scientific-pkg-gget--5220b2