mite_extras

Validation and conversion functionality for reaction SMARTS collected in the scope of MITE.

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

Installation

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 with hatch:

Input format: raw (MIBiG Submission Portal)

First, pre-format the raw input files:

• e.g. hatch run python input_file_splitter.py <new000.json>

Move the generated file(s) into a different directory (e.g. 'input')

• hatch run mite_extras -i input/ -o output/ -fin raw -fout json

This will convert all files into json-files following the MITE schema.

Input format: mite (MITE-formatted json)

To validate MITE entries or update them to a new schema version

• hatch run mite_extras -i input/ -o output/ -fin mite -fout json

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