Metadata-Version: 2.1
Name: pamogk
Version: 0.1.1
Summary: PAMOGK
Home-page: https://github.com/tastanlab/pamogk
Author: Fma
License: Creative Commons Attribution-Noncommercial-Share Alike license
Description: PAMOGK
        =====
        
        # Installation
        
        ## Getting the Code Base
        You can either checkout the code base through git:
        ```bash
        git clone https://github.com/tastanlab/pamogk.git
        ```
        or you can download the master branch from:
        > https://github.com/tastanlab/pamogk/archive/master.zip
        
        ## Python Environment
        Project mainly uses python, but some of the plot generation codes use matlab or output html files (plotly.js). Also some
         libraries might be dependent on operating system. In our tests we used Debian 12.04LTS and macOS Catalina.
        
        First install `pipenv` using the instructions given:
        
        > https://github.com/pypa/pipenv#installation
        
        We are using [pipenv](https://github.com/pypa/pipenv#installation) because of version locking and predictive builds.
        
        ## Setting up MOSEK
        We are using [MOSEK Optimizer API](https://docs.mosek.com/9.1/pythonapi/index.html) for optimizing view weights, and in
        order to use MOSEK you will need a license file. MOSEK provides free certificates for academic purposes and free trial
        certificates for Commercial usages. You can see check the link below for information on how to acquire an academic license:
        
        > https://www.mosek.com/products/academic-licenses/
        
        ### License File Placement
        You can either place the license file under user's home directory in a folder named `mosek` e.g:
        ```bash
        $HOME/mosek/mosec.lic # *nix/macOS users
        %USERPROFILE%\mosek\mosek.lic # windows users
        ```
        Other option is to set the `MOSEKLM_LICENSE_FILE` environment variable to your license file location.
        
        We also look for the license file paths in some custom paths (by overwriting `MOSEKLM_LICENSE_FILE` if not present).
        You can check `pamogk.config.MOSEK_SUPPORTED_PATHS` to see a list of supported paths.
        
        For more information:
        
        > https://docs.mosek.com/9.2/install/installation.html#setting-up-the-license
        
        ## Dependencies
        Install dependencies with:
        ```bash
        pipenv install
        ```
        
        ## Required Environment Variables
        You can add a `.env` file that will be loaded by `pipenv`
        
        Also please don't forget to export `MOSEKLM_LICENSE_FILE` variable as well if you are using a path other
        than `$HOME/mosek/mosek.lic`:
        
        ```bash
        # required for experiment running
        PYTHONPATH=${PYTHONPATH}:.
        MOSEKLM_LICENSE_FILE=$MY_MOSEK_LICENSE_FILE_PATH
        ```
        
        # Folder Structure
        - **pamogk:** package root folder
          - **kernels:** Kernel methods to calculate distance between patients. Will try to extend these!
          - **data_processor:** Data processors/converters used to convert different forms of data to usable forms.
           Will try to extend these!
          - **gene_mapper:** Uniprot/Entrez gene mapping matcher for different datasets using different gene IDs. Will try to
           separate to its own package or along with other tools.
          - **pathway_reader:** https://.ndexbio.org CX format, and http://kegg.jp KGML format reader and converters. Will try
           to separate to its own package or along with other tools.
        - **data:** Data files that are both raw or generated by the project. Keeping intermediate files saves a lot of
         computation time where applicable. (not included in package)
        - **experiments:** Experiments done on real data. (not included in package)
        
        
        # Experiments
        ## Running Experiments
        You should run experiments either by starting a pipenv environment shell by:
        ```bash
        pipenv shell
        ```
        
        or through pipenv with:
        ```bash
        pipenv run experiments/pamogk_all_exp_1.py
        ```
        This ensures that experiments are run with correct environment.
        
        ## Experiment Parameters
        Experiments are code entry points that have arguments that change per experiment. You can see their arguments by
         running them with `--help` parameter. e.g:
        ```bash
        ./experiments/pamogk_all_exp_1.py --help
        ```
        and you should see help as such:
        ```
        usage: pamogk_all_exp_1.py [-h] [--rs-patient-data file-path]
                                   [--rp-patient-data file-path]
                                   [--som-patient-data file-path]
        
        Run PAMOGK-mut algorithms on pathways
        
        optional arguments:
          -h, --help            show this help message and exit
          --rs-patient-data file-path, -rs file-path
                                rnaseq pathway ID list
          --rp-patient-data file-path, -rp file-path
                                rppa pathway ID list
          --som-patient-data file-path, -s file-path
                                som mut pathway ID list
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6.1
Description-Content-Type: text/markdown
