gget

Topics in the source

• gget
• Overview
• Installation
• Quick Start
• Module Categories
• 1. Reference & Gene Information
• gget ref - Reference Genome Downloads
• gget search - Gene Search

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. Install gget in a clean virtual environment to avoid conflicts: Basic usage pattern for all modules: 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) Retrieve download links and metadata for Ensembl reference genomes. Parameters: species: Genusspecies format (e.g., 'homosapiens', 'musmusculus'). Shortcuts: 'human', 'mouse' -w/--which: Specify return types (gtf, cdna, dna, cds, cdrna, pep). Default: all -r/--release: Ensembl

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