brsynth / rpvisualiser

Metabolic engineering visualizer

rpviz

Metabolic engineering visualizer

csv_network.py : To read information from a csv file sbml2list.py : To read information from a sbml file

smile2picture.py : To convert SMILES into svg image

network2json.py : To convert the network in a json file

1 html/pathway

py2html : To create an html file from a json file, using a template (in html/template.html) with jinja2 and to use it with

1 html updated for each pathway

py2html2 : To create a .js file with the json file and to open it with the template2 (in html/template2.html) and the network_viewer.js

nxvisualizer.py : To open the network directly in Cytoscape

Retropath2.0 wrapper

Implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: rules.csv, sink.csv and source.csv and produces results in an output folder.

Standalone

Prerequisites

• Python 3

Quick start

The main code is src/RetroPath2.py and can be run as the following:

python src/RetroPath2.py \
  -sinkfile <sink_file> \
  -sourcefile <source_file> \
  -max_steps 3 \
  -rulesfile <rules_file> \
  -topx 100 \
  -dmin 0 \
  -dmax 1000 \
  -mwmax_source 1000 \
  -mwmax_cof 1000 \
  -timeout 30 \
  -outdir <outdir_folder> \
  -is_forward False

Docker

RetroPath2 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
./RetroPath2.sh
  -sinkfile <sink_file> \
  -sourcefile <source_file> \
  -max_steps 3 \
  -rulesfile <rules_file> \
  -topx 100 \
  -dmin 0 \
  -dmax 1000 \
  -mwmax_source 1000 \
  -mwmax_cof 1000 \
  -timeout 30 \
  -outdir <outdir_folder> \
  -is_forward False

To call the tool with fresh code:

docker-compose run --rm -v <absolutepath_to_src>:/home/src retropath2

To call the tool from any location:

cd docker
docker-compose run --rm \
    -v <path/to/source.csv>:/home/source.csv:ro \
    -v <path/to/sink.csv>:/home/sink.csv:ro \
    -v <path/to/rules.csv>:/home/rules.csv:ro \
    -v <path/to/output_folder>:/home/outdir \
    -w /home \
    retropath2 python src/RetroPath2.py \
        -sinkfile <sink_file> \
        -sourcefile <source_file> \
        -max_steps 3 \
        -rulesfile <rules_file> \
        -topx 100 \
        -dmin 0 \
        -dmax 1000 \
        -mwmax_source 1000 \
        -mwmax_cof 1000 \
        -timeout 30 \
        -outdir <outdir_folder> \
        -is_forward False

Test

All modes can be tested with:

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

How to cite RetroPath2.0?

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