annocli

A command-line tool to query and download genome annotations from the Annotrieve API.

Installation

pip install annocli

From source:

git clone https://github.com/apollo994/annocli.git
cd annocli
pip install .
./test.sh

For development (includes pytest):

pip install -e ".[dev]"

Commands

annocli {COMMAND} --help

• download: Download annotations for given taxonomy IDs
• alias: Match sequence IDs between annotation and assembly files
• summary: Get information about features and biotypes available
• stats: Get summary statistics about gene and transcript features

For detailed usage examples, see USAGE.md.

Agent skill

skills/annotrieve/ is a skill that lets AI agents query, filter, compare and download Annotrieve annotations via annocli, the Annotrieve API and the gene-name search (annotrieve-xrefs). Install it by copying the folder into your agent skill directory (e.g. ~/.claude/skills/ for claude code).

Testing

Unit and component tests (mocked, no network):

pytest

End-to-end tests against the live Annotrieve API:

pytest -m e2e