lukasturcani/cagey

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.