Metadata-Version: 2.1
Name: metabolike
Version: 0.5.0
Summary: Build graph database from BRENDA and BioCyc for studying reprogrammed metabolisms.
Keywords: bioinformatics,metabolic-pathway,network,graph-database
Author-email: Yi Zhou <metabolike@y1zhou.com>
Requires-Python: >=3.8,<4
Description-Content-Type: text/x-rst
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python :: 3
Classifier: Framework :: FastAPI
Classifier: Framework :: Pytest
Classifier: Framework :: Sphinx
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Dist: lark>=0.11.3,<2.0.0
Requires-Dist: pandas>=1.0.0,<2.0.0
Requires-Dist: orjson>=3.6.2,<4.0.0
Requires-Dist: numpy>=1.22.0,<2.0.0
Requires-Dist: python-libsbml>=5.19.2
Requires-Dist: neo4j>=5.0.0
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Requires-Dist: requests>=2.28.0
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Requires-Dist: pytest ; extra == "test"
Requires-Dist: pytest-cov ; extra == "test"
Requires-Dist: pytest-mock ; extra == "test"
Requires-Dist: coverage<6.4 ; extra == "test"
Requires-Dist: coverage[toml]<6.4 ; extra == "test"
Requires-Dist: hypothesis>=6.47.0 ; extra == "test"
Requires-Dist: pytest-dotenv>=0.5.2 ; extra == "test"
Project-URL: Documentation, https://metabolike.readthedocs.io/
Project-URL: Source, https://github.com/y1zhou/metabolike
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: test

Metabolic reprogramming Knowledgebase
=====================================

.. image:: https://img.shields.io/pypi/v/metabolike
    :alt: PyPI release
    :target: https://pypi.org/project/metabolike/
.. image:: https://readthedocs.org/projects/metabolike/badge/?version=stable&style=flat
    :alt: Documentation status for stable version
    :target: https://metabolike.readthedocs.io/en/stable/
.. image:: https://img.shields.io/github/workflow/status/y1zhou/metabolike/PyTest?label=test
    :alt: PyTest workflow status
    :target: https://github.com/y1zhou/metabolike/actions/workflows/pytest.yml
.. image:: https://codecov.io/gh/y1zhou/metabolike/branch/main/graph/badge.svg
    :alt: Code coverage
    :target: https://codecov.io/gh/y1zhou/metabolike
.. image:: https://github.com/y1zhou/metabolike/workflows/CodeQL/badge.svg
    :alt: CodeQL analysis
    :target: https://github.com/y1zhou/metabolike/actions/workflows/codeql-analysis.yml
.. image:: https://img.shields.io/github/license/y1zhou/metabolike
    :alt: Package license
    :target: https://github.com/y1zhou/metabolike/blob/main/LICENSE
.. image:: https://img.shields.io/badge/code%20style-black-000000
    :alt: Code styled with Black
    :target: https://github.com/psf/black
.. image:: https://img.shields.io/github/commits-since/y1zhou/metabolike/latest/main
    :alt: GitHub commits since latest release (by date) for main branch
    :target: https://github.com/y1zhou/metabolike/commits/main

A Python package that aggregates the data from BRENDA_ and BioCyc_ into one unified `graph database`_.
The MetaCyc (BioCyc) database is imported to a graph database using the provided SBML file and various ``.dat`` files.
A `Streamlit`_ app is `included in the code`_ for easy route search with both example TCGA datasets and custom CSV files.

.. _BRENDA: https://brenda-enzymes.org/
.. _BioCyc: https://biocyc.org/
.. _graph database: https://neo4j.com/
.. _Streamlit: https://streamlit.io/
.. _included in the code: https://github.com/y1zhou/metabolike/blob/main/metabolike/api/main.py

To-Do
-----

* Add tutorial for the package
* Add Dockerfile and docker-compose file

