gget

Original：🇺🇸 English

Translated

gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.

4installs

Sourceaffaan-m/everything-claude-code

Added on2026-05-12

NPX Install

npx skill4agent add affaan-m/everything-claude-code gget

SKILL.md Content

View Translation Comparison →

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

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:

bash

gget <module> [arguments] [options]

Python shape:

python

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:

bash

gget search -s human brca1 dna repair -o brca1-search.json

Fetch gene metadata:

bash

gget info ENSG00000012048 -o brca1-info.json

Fetch a sequence:

bash

gget seq ENSG00000012048 -o brca1-seq.fa

Run a small BLAST query:

bash

gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json

Python example:

python

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.

markdown

| 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?

gget

NPX Install

Tags

SKILL.md Content

gget

When to Use

Installation

Basic Patterns

Common Modules

Quick Examples

Reproducibility Log

Review Checklist

References