rpCompletion

Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rrCache which store pre-computed data.

All metabolic pathways will be built as the following:

• In each "master" pathway,
  • each chemical transformation could be produced by multiple reaction rules, and
    • each reaction rule could have been produced by multiple template chemical reactions.

Thus, each different template reaction for each different reaction rule for each different chemical transformation provides one single possible pathway. The algorithm explores the combinatorics of all possible pathways and for each "master pathway" (the one from chemical transformations), keeps only top ones (defined by max_subpaths_filter CLI option, default: 10).

Input

Required:

• rp2_metnet: (string) Path to the metabolic network file built by RetroPath2.0
• sink: (string) Path to the rpextractsink file containing infos on molecules in the sink
• rp2paths_compounds: (string) Path to the rp2paths compounds file
• rp2paths_pathways: (string) Path to the rp2paths pathways file
• outdir: (string) Path to the folder where result files are written

Advanced options:

• --upper_flux_bound: (integer, default=10000) Upper flux bound value for all new reactions created
• --lower_flux_bound: (integer, default=-10000) Lower flux bound value for all new reactions created
• --max_subpaths_filter: (integer, default=10) Number of subpaths per master pathway

Installation Guide

Overview

rpcompletion 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 rpcompletion

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Apple Silicon macOS (M1/M2/M3)

1. Install Rosetta 2

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

2. Install rpLibs

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

Or with mamba:

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

3. Persist platform setting

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

5. Verify installation

python -c "import rpcompletion; print('rpcompletion installed successfully')"
python -c "import cobra; print(cobra.__version__)"

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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

rpCompletion process

From Python code

from rpcompletion import rp_completion

pathways = rp_completion(
    rp2_metnet_filename,
    sink_filename,
    rp2paths_compounds_filename,
    rp2paths_pathways_filename,
)

From CLI

python -m rpcompletion \
  rp2_metnet.csv \
  sink.csv \
  rp2paths_compounds.csv \
  rp2paths_pathways.csv \
  <outdir>

Tests

Test can be run with the following commands:

Natively

python -m pytest

Authors

• Joan Hérisson

Acknowledgments

• Thomas Duigou
• Melchior du Lac

Licence

rpCompletion is released under the MIT licence. See the LICENCE file for details.