Metadata-Version: 2.1
Name: rp2paths
Version: 1.5.0
Summary: 'retropath2.0 to pathways'
Home-page: https://github.com/brsynth/rp2paths
Author: 'thomas duigou'
Author-email: thomas.duigou@inrae.fr
License: MIT
Description: # RP2paths -- RetroPath2.0 to pathways
        
        [![Anaconda-Server Badge](https://anaconda.org/brsynth/rp2paths/badges/latest_release_date.svg)](https://anaconda.org/brsynth/rp2paths)
        [![Anaconda-Server Badge](https://anaconda.org/brsynth/rp2paths/badges/version.svg)](https://anaconda.org/brsynth/rp2paths)
        
        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.
        
        ## Installation
        
        ### Prerequisites
        
        rp2paths relies on several packages (rdkit, cairo) and binaries (java, graphviz) that can't be installed directly with pip. Please install them before pursuing the rp2paths set up:
        
        ```bash
        # from a new <myenv> conda environment
        conda create --name <myenv> python=3
        conda install --yes --channel rdkit rdkit cairo
        conda install --yes --channel cyclus java-jre
        conda install --yes --channel conda-forge graphviz
        ```
        
        
        ### From pip
        ```bash
        # installation in an already existing <myenv> environment (see prerequisites)
        conda activate <myenv>
        python -m pip install rp2paths
        ```
        
        ### From conda
        ```bash
        # installation in an already existing <myenv> environment (see prerequisites)
        conda activate <myenv>
        conda install -c brsynth 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
        
        ```bash
        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:
        
        ```bash
        source activate <myenv>
        python -m rp2paths all examples/naringenin/rp2-results.csv --outdir examples/naringenin/outdir
        ````
        
        
        ## For developers
        
        ### Development installation
        
        After a git clone:
        ```bash
        cd <repository>
        conda create --name <dev_env> python=3
        conda install --name <dev_env> --yes --channel rdkit rdkit cairo
        conda install --name <dev_env> --yes --channel cyclus java-jre
        conda install --name <dev_env> --yes --channel conda-forge graphviz flake8
        conda install --name <dev_env> --yes pytest
        conda develop --name <dev_env> .
        ```
        
        ### Tests
        
        Using Docker containers with:
        ```
        cd tests
        ./test-in-docker.sh [file_to_test]
        ```
        
        Without using Docker containers:
        ```
        cd tests
        conda activate <dev_env>
        pytest [file_to_test]
        ```
        
        
        ## 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.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.5
Description-Content-Type: text/markdown
