# Gget

Fast CLI/Python queries to 20+ bioinformatics databases.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Data and ML
- License: BSD-2-Clause license
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill gget -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill gget -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill gget -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill gget -g -a gemini-cli -y`

## Description

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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:

```bash
# 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:

```bash
# 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**:
```bash
# List available species
gget ref --list_species

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/gget/SKILL.md