rpScore

Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.

Input

Positional argument:

• infile: (string) Path to pathway (rpSBML) file
• outfile: (string, required if one single input file is passed) path to store the scored pathway

Optional arguments:

• --no_of_rxns_thres: (int, default=10) number of reactions above which a pathway is not scored (too long)
• --data_train_file: (string) path to the trained data
• --log: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'
• --version: Display program's version and exit

Installation Guide

Overview

rpthermo depends on rplibs, which depends on cobra, which requires python-libsbml.
On Apple Silicon (arm64) macOS, python-libsbml is not available as a native Conda package.

Therefore, installation must be done using an Intel (osx-64) Conda environment under Rosetta.

---

General case

conda install -c conda-forge rpthermo

---

Apple Silicon macOS (M1/M2/M3)

1. Install Rosetta 2

softwareupdate --install-rosetta --agree-to-license

2. Install

CONDA_SUBDIR=osx-64 conda install -c conda-forge rpfba

Or with mamba:

CONDA_SUBDIR=osx-64 mamba install -c conda-forge rpfba

3. Persist platform setting

conda config --env --set subdir osx-64

4. Verify installation

python -c "import rpfba; print('rpfba installed successfully')"

5. (Optional) Dev installation

CONDA_SUBDIR=osx-64 conda env create -f environment.yaml

---

Troubleshooting

Solver fails on Apple Silicon

Make sure you are using:

CONDA_SUBDIR=osx-64

Wrong architecture environment

Check:

conda config --show subdir

Expected output:

subdir: osx-64

Run

From Python code

from rpscore import predict_score
from rplibs import rpPathway

pathway = rpPathway(
    infile='tests/rpscore/data/pathway.xml'
)

global_score = predict_score(pathway)

From CLI

python -m rpscore <input_rpsbml> <output_rpsbml>

Tests

Test can be run with the following commands:

Natively

cd tests
pytest -v

CI/CD

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

Authors

• Jean-Loup Faulon
• Joan Hérisson

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Thomas Duigou