brsynth/rpcofactors repository overview

⁠rpCofactors

• Docker Image: brsynth/rpcofactors-standalone⁠

Completes monocomponent reaction output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input may be a single SBML file or a collection within a tar.xz archive

⁠Input

Required:

• -input: (string) Path to the input file. Can be either a single SBML file or a collection as a tar.xz archive file
• -input_format: (string)

Advanced Options:

• -pathway_id: (string, default: rp_pathway) ID of the heterologous pathway
• -compartment_id: (string, default: MNXC3 (i.e. cytoplasm)) ID of the SBML compartment where the heterologous pathway will be expressed in (default: MNXC3 (i.e. cytoplasm))

⁠Output

• -output: (string) Path to the output file

⁠Dependencies

• Base docker image: brsynth/rpBase⁠
• Cache docker image: brsynth/rpCache⁠

⁠Building the docker

To build the docker locally, run the following command in the project directory:

docker build -t brsynth/rpcofactors-standalone .

⁠Running the test

To test untar the test.tar.xz file and run the following command:

python run.py -input test/test_rpReader.tar -output test/test_rpCofactors.tar -input_format tar

⁠Contributing

Please read CONTRIBUTING.md⁠ for details on our code of conduct, and the process for submitting pull requests to us.

⁠Versioning

v0.1

⁠Authors

• Melchior du Lac

⁠License

This project is licensed under the MIT License - see the LICENSE.md⁠ file for details

⁠Acknowledgments

• Thomas Duigou
• Joan Hérisson

⁠How to cite rpCofactors?