Docs

https://cagey.readthedocs.io

Cagey

First and foremost cagey is a command line tool for creating and managing a cage database. With cagey you will extract a a range of experimental and computational data in a variety of formats and place it into a single file. You can then use this file as input for your scripts which perform data analysis. You can install cagey with:

pip install cagey

Once installed you can use the command line tool to create a new database:

cagey new path/to/data path/to/cagey.db

This will create a new database at path/to/cagey.db and populate it with data from path/to/data. There are in fact a lot more things you can do with cagey, and the best way to learn about them is to use it interactively, starting with:

cagey --help

Usage: cagey [OPTIONS] COMMAND [ARGS]...

A cage database tool.
Run cagey help intro for an introduction.

╭─ Options ───────────────────────────────────────────────────────────────────────────╮ │ --install-completion Install completion for the current shell. │ │ --show-completion Show completion for the current shell, to copy it or │ │ customize the installation. │ │ --help Show this message and exit. │ ╰─────────────────────────────────────────────────────────────────────────────────────╯ ╭─ Commands ──────────────────────────────────────────────────────────────────────────╮ │ help Get help on how to use cagey. │ │ insert Insert new data into the cagey database. │ │ ms Mass spectrum analysis. │ │ new Create a new database. │ │ nmr Extract NMR peaks. │ ╰─────────────────────────────────────────────────────────────────────────────────────╯

Working with the database

Once you've used cagey to create a database, you can use the cagey.queries module to extract data from it in your Python scripts. This step is best understood by reading our documentation, which you can find at https://cagey.readthedocs.io.