Metadata-Version: 2.1
Name: keggtools
Version: 0.4.0
Summary: Enrichment analysis and visualisation toolkit for KEGG pathways
Home-page: https://github.com/harryhaller001/keggtools
Author: harryhaller001
Author-email: harryhaller001@gmail.com
License: MIT
Description: # keggtools
        Library for KEGG pathway enrichment analysis.
        
        ## Installation
        
        `keggtools` only supports `python` version greater than or equal `3.6`.
        
        Dependencies
        
        * `graphviz`
        
        Install graphviz on `Ubuntu`. More graphviz install options [https://www.graphviz.org/download/](https://www.graphviz.org/download/)
        ```bash
        # pydot is needed for rendering of pathways and required graphviz
        sudo apt install graphviz
        ```
        
        Python dependencies
        
        * `requests`
        * `tqdm`
        * `pydot`
        * `scipy`
        
        Installation of python dependencies:
        
        ```bash
        python3 -m pip install requests tqdm pydot scipy
        ```
        
        
        Installation `keggtools` PyPI package using `pip`:
        
        ```bash
        python3 -m pip install keggtools
        ```
        
        Installation `keggtools` from Github source:
        
        ```bash
        python3 -m pip install git+git@github.com:harryhaller001/keggtools.git
        ```
        
        Installation `keggtools` from release source:
        
        ```bash
        # TODO add release
        ```
        
        
        ## API
        
        ### Download and caching
        
        
        ```python
        from keggtools.resolver import KEGGPathwayResolver
        
        # Get all components
        print(KEGGPathwayResolver.get_components())
        
        # List all pathways
        
        # TODO: check taxid exists
        organism_id = 10090
        
        resolver = KEGGPathwayResolver(organism_id)
        
        # TODO: maybe move to static methods
        print(resolver.get_pathway_list())
        ```
        
        
        ### Parsing
        
        
        
        ### Enrichment and Testing
        
        
        
        ### Rendering
        
        
        ## Development
        
        Fast install with `virtualenv` for development.
        
        ```bash
        python3 -m virtualenv venv
        source ./venv/bin/activate
        pip install --upgrade pip
        pip install -r requirements.txt
        ```
        
        
        
        ### Testing
        
        Run unittest to verify `keggtools` installation
        
        ```bash
        # TODO: implement unittest
        ```
        
        ### Static code analysis
        
        Static code analysis using mypy
        
        ```bash
        # Install mypy
        pip install mypy
        
        # Or
        pip install -r dev_requirements.txt
        ```
        
        Windows
        
        ```bash
        # Testing setup.py and package
        mypy setup.py
        python setup.py install
        # mypy --python-executable E:\Github\keggtools\venv\Scripts\python.exe -p keggtools --ignore-missing-imports
        mypy -p keggtools
        ```
        
        Linux
        
        ```bash
        mypy setup.py
        python3 setup.py install
        mypy -p keggtools
        ```
        
        
        ## Build process
        
        Build package
        
        ```bash
        # Build .egg, .whl and .tar
        python setup.py sdist bdist_wheel
        ```
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
