brsynth/rp2paths-new repository overview

⁠RP2paths -- RetroPath2.0 to pathways

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

⁠Standalone

⁠Prerequisites

• Python 3

⁠Installation

Installation steps are described in the INSTALL file.

⁠Quick start

The main code is src/RP2paths.py. Once a scope has been produced by RetroPath2.0, a typical command line for extracting the pathways from the results is:

python src/RP2paths.py all results.csv --outdir pathways

where:

• all specify that all the tasks needed for retreiving pathways will be executed at once.
• results.csv is the metabolic space outputted by the RetroPath2.0 workflow.
• --outdir pathways specify the directory in which all files will be outputted (here in pathways subfolder).

Additional options are described in the embedded help

python src/RP2paths.py -h
python src/RP2paths.py all -h

In the output folder (here pathways), 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).

⁠Examples

Precomputed result files (i.e. 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:

1. If needed, activate the python environment (here named pyenv) that provides all the mandatory python library (see the installation section for details):

source activate pyenv

1. Retrieve pathways:

python src/RP2paths.py all examples/naringenin/rp2-results.csv --outdir examples/naringenin/pathways

⁠Docker

RP2Paths can be run into a docker container.

⁠Prerequisites

• Docker - Install⁠

⁠Installation

Before running the container, the image has to be built with:

cd docker
docker-compose build

⁠Run

Then, the tool is runnable by:

cd docker
./RP2paths.sh all <path_to_rp2-results.csv> --outdir <path_to_out_pathways>

To call the tool with fresh code:

docker-compose run --rm -v <absolutepath_to_src>:/home/src rp2paths

To call the tool from any location:

docker run \
    --rm \
    --volume <path_to_rp2-results.csv>:/home/input.csv:ro \
    --volume <path_to_output_folder>:/home/outdir \
    --workdir /home \
    brsynth/rp2paths python src/RP2paths.py all input.csv --outdir outdir

⁠Test

All modes can be tested with:

cd test
./run[-in-docker].sh

⁠How to cite RP2paths?

Please cite:

Delépine 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.