| name | ecc-gget |
| description | gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs. |
| origin | community |
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-check the module
docs. The upstream databases queried by gget change over time.
Basic Patterns
CLI shape:
gget <module> [arguments] [options]
Python shape:
import gget
result = gget.search(["BRCA1"], species="human")
print(result)
Common workflow:
- Identify the species, assembly, gene ID type, and database needed.
- Check the current module documentation for arguments.
- Run a small query first.
- Save output with an explicit filename and date.
- 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.gget enrichr, gget opentargets, gget archs4, gget bgee, gget cbio,
and gget cosmic: explore enrichment, target, expression, cancer, and disease
association data.
Do not assume every module supports every Python version or dependency set.
Some optional scientific dependencies have narrower version support than the
core package.
Quick Examples
Find genes:
gget search -s human brca1 dna repair -o brca1-search.json
Fetch gene metadata:
gget info ENSG00000012048 -o brca1-info.json
Fetch a sequence:
gget seq ENSG00000012048 -o brca1-seq.fa
Run a small BLAST query:
gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json
Python example:
import gget
genes = gget.search(["BRCA1", "DNA repair"], species="human")
info = gget.info(["ENSG00000012048"])
sequence = gget.seq("ENSG00000012048")
Reproducibility Log
For scientific outputs, include enough metadata to replay the query.
| Date | gget version | Module | Query | Species/assembly | Output | Notes |
| --- | --- | --- | --- | --- | --- | --- |
| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |
Also record:
- Python version and environment manager.
- Any optional dependency installed through
gget setup.
- Database-specific identifiers returned by the query.
- Whether output is JSON, CSV, FASTA, or a DataFrame export.
- Any failures that were resolved by upgrading
gget.
Review Checklist
- Did you upgrade or verify the installed
gget version?
- Did you check the current upstream module docs before using arguments?
- Is the species or assembly explicit?
- Are identifiers preserved exactly, including Ensembl/UniProt prefixes?
- Is the result labeled as database output rather than clinical interpretation?
- Is the query reproducible from the saved command or Python snippet?
- Are optional dependencies installed in an isolated environment?
References
