gget
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.
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About gget
gget is an innovative command-line tool and Python package designed to streamline access to over 20 bioinformatics databases, making it easier for researchers and practitioners to perform quick lookups on gene information, sequence analysis, protein structures, and more. The skill addresses the common need for efficient querying of genomic data, allowing users to retrieve essential information swiftly and with minimal setup, thus enhancing productivity in bioinformatics research and analysis tasks. Its straightforward command-line interface and Python integration ensure that both novice and experienced users can utilize its capabilities without extensive learning curves.
FAQ
How do I install gget?
You can install gget using pip in a clean virtual environment. Recommended command: 'uv pip install gget'.
What formats can gget return results in?
gget can return results in JSON format by default or CSV format when using the '-csv' flag.
Is there a limit on the number of IDs I can query with gget info?
Yes, the gget info command supports up to approximately 1000 Ensembl IDs.
Can I use gget for batch processing?
gget is best suited for interactive exploration and simple queries. For batch processing, consider using biopython.
Which databases does gget support?
gget provides access to over 20 genomic databases, including Ensembl, UniProt, and NCBI.
Install gget
Quick Setup:
- Copy the skill folder to
.claude/skills/ - Claude will automatically detect and use the skill
Repository
K-Dense-AI/claude-scientific-skills