gget

Overview

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, viral sequences, expression data, disease associations, and mouse tissue/cell specificity metrics through a consistent interface. Most gget modules work both as command-line tools and as Python functions.

Important: The databases queried by gget are continuously updated, which sometimes changes their structure. Guidance here targets gget 0.30.5 (PyPI current as of 2026-06-07). For reproducible work, pin gget==0.30.5; for broken upstream database adapters, update gget after checking release notes.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Reproducible install targeting this skill
uv venv .venv
source .venv/bin/activate
uv pip install "gget==0.30.5"

# In Python/Jupyter
import gget

Quick Start

Basic usage pattern for all modules:

# Command-line
gget <module> [arguments] [options]

# Python
gget.module(arguments, options)

Most modules return:

• Command-line: JSON (default) or CSV with -csv flag
• Python: DataFrame or dictionary

Common flags across modules:

• -o/--out: Save results to file
• -q/--quiet: Suppress progress information
• -csv: Return CSV format (command-line only)

Python argument names generally match long CLI options without leading dashes. For example, becomes . Use for the exact current signature.