| Name | mite-extras JSON |
| Version |
1.4.1
JSON |
| download |
| home_page | None |
| Summary | Parsing, conversion, and validation functionality for Minimum Information about a Tailoring Enzyme (MITE) files. |
| upload_time | 2025-02-13 16:04:39 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.12 |
| license | None |
| keywords |
cheminformatics
genomics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
mite_extras
==========
[](https://doi.org/10.5281/zenodo.13941745) [](https://badge.fury.io/py/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](https://github.com/mite-standard).
## 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](https://github.com/mmzdouc/mite_extras)
- 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`
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