RP2paths -- RetroPath2.0 to pathways

RP2paths extracts the set of pathways that lies in a metabolic space file outputted by the RetroPath2.0 workflow. RetroPath2.0 is freely accessible on myExperiment.org at: https://www.myexperiment.org/workflows/4987.html.

Installation

From conda

# installation in an already existing <myenv> environment (see prerequisites)
conda activate <myenv>
conda install -c brsynth -c conda-forge rp2paths

Usage

From CLI

Once a scope has been produced by RetroPath2.0, a typical command line for extracting the pathways from the results is

python -m rp2paths all <retropath2_scope> [--outdir <outdir>]

where:

• all specify that all the tasks needed for retrieving pathways will be executed at once.
• <retropath2_scope> is the metabolic space outputted by the RetroPath2.0 workflow.
• --outdir <outdir> specify the directory in which all files will be outputted.

In the <outdir> folder, the complete set of pathways enumerated will be written in the out_paths.csv file. In addition, for each pathway there will be a .dot file (.dot representation of the graph) and a .svg file (.svg depiction of the pathway).

Available options

Additional options are described in the embedded help:

# List of possible modes
python -m rp2paths -h

# List of options for the all-in-one mode
python -m rp2paths all -h

Examples

Precomputed results (outputted by RetroPath2.0) are provided in the examples folder for few compounds (carotene, naringenin, pinocembrin, violacein).

Below are the command lines for generating pathways that lie in naringenin result file:

source activate <myenv>
python -m rp2paths all examples/naringenin/rp2-results.csv --outdir examples/naringenin/outdir

No scope warnings

A warning message WARNING: *** Scope Task: no scope matrix was produced, exit indicates that no reaction have been indified as being part of a pathway. This can happen when the retrosynthesis exploration performed by RetroPath2.0 does not reach a minimal set of sink compounds.

For developers

Development installation

After a git clone:

cd <repository>
conda env create -f environment.yaml -n <dev_env>
conda develop -n <dev_env> .
conda activate <dev_env>

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).

How to cite RP2paths?

Please cite:

Delepine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002

Licence

RP2paths is released under the MIT licence. See the LICENCE.txt file for details.