brsynth/rpcompletion repository overview

⁠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 rpCache which store pre-computed data.

⁠Input

Required:

• -rp2paths_pathways: (string) Path to the rp2paths pathways file
• -rp2paths_compounds: (string) Path to the rp2paths compounds file
• -rp2_pathways: (string) Path to the RetroPath2.0 pathways file

Advanced options:

• -upper_flux_bound: (integer, default=9999) Upper flux bound value
• -lower_flux_bound: (integer, default=0) Lower flux bound value
• -maxSubPaths_filter: (integer, default=10) Number of subpaths per path
• -pathway_id: (string, default=rp_pathway) ID of the heterologous pathway
• -compartment_id: (string, default=MNXC3 (i.e. cytoplasm)) Heterologous pathway compartment ID
• -species_group_id: (string, default=central_species) ID of the central species, i.e. not cofactors, in the heterologous reactions
• -sm: (optional, string, default: file) Store mode. If 'file', rpCache is supposed to be stored in files. Else, the rpCache is supposed to be stored in a Redis database which the name is the value of this input field.

⁠Output

• -outputTar: (string) Path to the output tar.xz file

⁠Standalone Mode

⁠Prerequisites

• Python 3 (with requests module)

⁠Quick start

The main code is src/rpCompletion.py. Once a scope has been produced by RP2Paths, a typical command line for completing the pathways from the results is:

python3 ../src/rpCompletion.py \
  -rp2_pathways rp2_pathways.csv \
  -rp2paths_pathways rp2paths_pathways.csv \
  -rp2paths_compounds rp2paths_compounds.csv \
  -output out \
  -maxSubPaths_filter 10 \
  -sm db

where:

• -rp2_pathways is the metabolic space outputted by the RetroPath2.0 workflow.
• -rp2paths_pathways is the set of pathways outputted by the RP2Paths tool.
• -rp2paths_compounds is the set of compounds outputted by the RP2Paths tool.
• --output specify the directory in which all files will be outputted.

⁠Test

Some tests can be runned. To do so, please follow insructions below:

cd test
./run.sh [small | normal | big] <max_subpaths>

The first parameter indicates the dataset to use, the second indicates the maxSubPaths_filter option.

⁠Docker Mode

rpCompletion can be run into a docker container.

⁠Prerequisites

• Docker - Install⁠
• rpCache: brsynth/rpCache <https://hub.docker.com/r/brsynth/rpcache>_

⁠Build image

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
./rpCompletion.sh <absolute_indata_folder>

Inside the container, rpCompletion can be run following the Standalone Mode.

⁠Test

All modes can be tested with:

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

⁠Authors

• Melchior du Lac
• Joan Hérisson

⁠Acknowledgments

• Thomas Duigou

⁠How to cite rpCompletion?

⁠Licence

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

• Docker image: brsynth/rpcompletion⁠