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
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
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/pytfa.git /path/to/pytfa
cd /path/to/pytfa
git lfs install
git lfs pullThis 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)
This module requires COBRApy, as well as 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.
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.
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
pip3 install pytfaor from source
git clone https://github.com/EPFL-LCSB/pytfa.git /path/to/pytfa
pip3 install -e /path/to/pytfaThree 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.
Documentation is hosted at Read the Docs
Alternatively you can also generate the docs locally.
Make sure sphinx is installed, and install as well the 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.
We recommend using the Docker container for testing the code, as it comes with everything bundled.
Install pytest if you don't
already have it (pip install pytest, already included in the
container), then start the tests with the pytest command.
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,
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
for more information about this.
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.
Here is an example script :
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()The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
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