mite-extras

mite_extras

This package contains functionality to validate entries of the Minimum Information about a Tailoring Enzyme (MITE) repository.

This includes:

• Validation of the MITE json format (does the entry follow the mite_schema format)
• Validation of reaction SMARTS (does the reaction SMARTS lead to the expected product when applied to a specified substrate)
• Sanitation of SMILES and reaction SMARTS
• Fetching of NCBI GenPept/UniProtKB IDs

When used as CLI, mite_extras can automatically update MITE entries (see below). However, it can also be used as a library (e.g. as done in mite_data).

For more information, see the README of the MITE-Standard organisation page.

Installation

Attention: this program has only been tested with Ubuntu Linux.

With pip from PyPI

• Install with pip install mite_extras

With hatch from GitHub

• Install python 3.12.x
• Install hatch (e.g. with pipx install hatch)
• Download or clone the repository
• Run hatch -v env create

Quick Start: Example

Run from command line:

To validate MITE entries or update them to a new schema version (requires mite_extras to be installed via pip).

• mite_extras -i <input/> -o <output/>

Run with hatch:

Validate MITE entries or update them to a new schema version

• hatch run mite_extras -i input/ -o output/

For devs

• Install developer dependencies with hatch -v env create dev
• Initialize pre-commit with hatch run dev:pre-commit install
• Run tests with hatch run dev:pytest
• Run CLI with hatch run dev:mite_extras and the appropriate options
• If necessary, remove the environment again with hatch env remove dev