gget

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, expression data, and disease associations through a consistent interface. All 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. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Using uv (recommended)
uv uv pip install gget

# Or using pip
uv pip install --upgrade gget

# 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)

Module Categories

1. Reference & Gene Information

gget ref - Reference Genome Downloads

Retrieve download links and metadata for Ensembl reference genomes.

Parameters:

• species: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
• -w/--which: Specify return types (gtf, cdna, dna, cds, cdrna, pep). Default: all
• -r/--release: Ensembl release number (default: latest)
• -l/--list_species: List available vertebrate species
• -liv/--list_iv_species: List available invertebrate species
• -ftp: Return only FTP links
• -d/--download: Download files (requires curl)

Examples:

# List available species
gget ref --list_species

# Get all reference files for human
gget ref homo_sapiens

# Download only GTF annotation for mouse
gget ref -w gtf -d mouse