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: ```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_sapien...