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EPFL-LCSB / pytfa

A Python 3 implementation of Thermodynamics-based Flux Analysis
https://lcsb.epfl.ch/
Apache License 2.0
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pyTFA

|PyPI| |Documentation Status| |Build Status| |Codecov| |Codacy branch grade| |license|

Thermodynamics-based Flux Analysis, in Python. Paper : Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis. "pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis" Bioinformatics (2018), bty499, DOI: https://doi.org/10.1093/bioinformatics/bty499 <https://doi.org/10.1093/bioinformatics/bty499>_

Implements: Christopher S. Henry, Linda J. Broadbelt, and Vassily Hatzimanikatis. "Thermodynamics-based metabolic flux analysis." Biophysical journal 92.5 (2007): 1792-1805. DOI: https://doi.org/10.1529/biophysj.106.093138 <https://doi.org/10.1529/biophysj.106.093138>__

Requirements

You will need to have Git-LFS <https://git-lfs.github.com/>_ in order to properly download some binary files:

.. code:: bash

git clone https://github.com/EPFL-LCSB/pytfa.git /path/to/pytfa
cd /path/to/pytfa
git lfs install
git lfs pull

This module was developed in Python 3.5, and it is recommended to run Python 3.5 to run commercial solvers such as Gurobi and CPLEX. Other Python versions (2.7, 3.4) should also work (see the CI builds <https://travis-ci.org/EPFL-LCSB/pytfa>_)

This module requires COBRApy <https://github.com/opencobra/cobrapy/>, as well as optlang <https://github.com/biosustain/optlang> to work properly. The installer should take care of that for you. You might also want to install a dedicated solver. GLPK, CPLEX and Gurobi are supported.

Container-based install

You might want to use this program inside of a container. The |docker|_ subfolder has all the necessary information and source files to set it up.

.. |docker| replace:: docker/ .. _docker: https://github.com/EPFL-LCSB/pytfa/tree/master/docker

Setup

This step is not required if you're using the container, which bundles all this.

You can install this module with pip:

For Python 3, you might have to use pip3 instead of pip

.. code:: bash

pip3 install pytfa

or from source

.. code:: bash

git clone https://github.com/EPFL-LCSB/pytfa.git /path/to/pytfa
pip3 install -e /path/to/pytfa

Quick start

Three tutorial files detail thoroughly normal usages of the pytfa package. They can be found at:

::

pytfa
└── tutorials
    ├── figure_paper.py
    ├── tutorial_basics.py
    └── tutorial_sampling.py

More information can be found here <http://pytfa.readthedocs.io/en/latest/quickstart.html>__.

Documentation

Documentation is hosted at Read the Docs <http://pytfa.readthedocs.io/en/latest/index.html>__

Alternatively you can also generate the docs locally.

Make sure sphinx <https://www.sphinx-doc.org/en/stable/> is installed, and install as well the theme <https://github.com/rtfd/sphinx_rtd_theme> (this is already bundled with the container):

::

pip install sphinx sphinx-rtd-theme

You can then generate the documentation with this command:

::

cd work/pytfa/doc && make html

The resulting HTML files will be located in work/pytfa/doc/_build.

Testing the code

We recommend using the Docker container <https://github.com/EPFL-LCSB/pytfa/tree/master/docker>__ for testing the code, as it comes with everything bundled.

Install pytest <https://docs.pytest.org/en/latest/>__ if you don't already have it (pip install pytest, already included in the container), then start the tests with the pytest command.

Usage

First, create your COBRApy model. Make sure to define the additional values required by pyTFA, as said in the "Models" page of the documentation.

If you already have a Matlab model with thermodynamic data, you might want to use pytfa.io.import_matlab_model. Otherwise, have a look at the COBRApy documentation <https://cobrapy.readthedocs.io/en/latest/io.html#MATLAB>__, then add the required properties.

If you're using a specific solver, don't forget to tell COBRApy about it by setting the solver property of your model to the name of your solver. See the COBRApy documentation <https://cobrapy.readthedocs.io/en/latest/solvers.html>__ for more information about this.

Thermodynamic database

You also need a thermodynamic database. Use thermoDBconverter.py if you have a thermodynamic database from Matlab you wish to import to Python.

Thermodynamic databases are stored in .thermodb files and can be easily loaded with pytfa.io.load_thermoDB.

Example script

Here is an example script :

.. code:: python

import pytfa
from pytfa.io import import_matlab_model, load_thermoDB

cobra_model = import_matlab_model('../models/small_yeast.mat')

thermo_data = load_thermoDB('../data/thermo_data.thermodb')

mytfa = pytfa.ThermoModel(thermo_data, cobra_model)
mytfa.solver = 'optlang-cplex'

## TFA conversion
mytfa.prepare()
mytfa.convert()

## Info on the model
mytfa.print_info()

## Optimality
tfa_solution = mytfa.optimize()

.. |PyPI| image:: https://img.shields.io/pypi/v/pytfa.svg :target: https://pypi.org/project/pytfa/ .. |Documentation Status| image:: https://readthedocs.org/projects/pytfa/badge/?version=latest :target: http://pytfa.readthedocs.io/en/latest/?badge=latest .. |license| image:: http://img.shields.io/badge/license-APACHE2-blue.svg :target: https://github.com/EPFL-LCSB/pytfa/blob/master/LICENSE.txt .. |Build Status| image:: https://travis-ci.com/EPFL-LCSB/pytfa.svg?branch=master :target: https://travis-ci.com/EPFL-LCSB/pytfa .. |Codecov| image:: https://img.shields.io/codecov/c/github/EPFL-LCSB/pytfa.svg :target: https://codecov.io/gh/EPFL-LCSB/pytfa .. |Codacy branch grade| image:: https://img.shields.io/codacy/grade/d8fd67ee134d46a69115c9b39c19be26/master.svg :target: https://www.codacy.com/app/realLCSB/pytfa .. |Code climate| image:: https://img.shields.io/codeclimate/github/EPFL-LCSB/pytfa.svg :target: https://codeclimate.com/github/EPFL-LCSB/pytfa

License

The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE <https://github.com/EPFL-LCSB/pytfa/blob/master/LICENSE.txt>_ file for more details.