Metadata-Version: 1.1
Name: probabilistic2020
Version: 1.0.4
Summary: Probabilistic 20/20
Home-page: https://github.com/KarchinLab/probabilistic2020
Author: Collin Tokheim
Author-email: fake@gmail.com
License: JHU Academic Software License Agreement (free for non-commercial use)
Description: Probabilistic 20/20
        ===================
        
        The Probabibilistic 20/20 test identifies genes with signficant oncogene-like and tumor suppressor gene-like mutational patterns for small coding region variants. 
        Putative signficant oncogenes are found through evaluating 
        missense mutation clustering and *in silico* pathogenicity scores. Often highly clustered missense
        mutations are indicative of activating mutations.
        While statistically signficant tumor suppressor genes (TSGs) are found by abnormally high proportion of inactivating mutations.
        
        Probabilistic 20/20 evaluates statistical significance by employing 
        monte carlo simulations, which incorporates observed mutation context. Monte carlo
        simulations are performed within the same gene and thus avoid building a background
        distribution based on other genes. This means that the statistical test can be applied 
        to either all genes in the exome from exome sequencing or to a certain target set of genes
        from targeted sequencing.
        
        The Probabilistic 20/20 test has nice properties since it accounts
        for several factors that could effect the significance of driver genes.
        
        * gene length
        * mutation context
        * gene sequence (e.g. codon bias)
        
        Documentation
        -------------
        
        .. image:: http://readthedocs.org/projects/probabilistic2020/badge/?version=latest
            :target: http://probabilistic2020.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        Please see the `documentation <http://probabilistic2020.readthedocs.org/>`_ on readthedocs for more details.
        
        
        Installation
        ------------
        
        .. image:: https://travis-ci.org/KarchinLab/probabilistic2020.svg?branch=master
            :target: https://travis-ci.org/KarchinLab/probabilistic2020
        
        
        Python Package Installation
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Using the python package installation, all the required python packages for the probabibilistic 20/20 test will automatically be installed for you.
        
        To install the package into python you can use `pip`. If you are installing to a system wide python then you may need to use `sudo` before the pip command.
        
        .. code-block:: bash
        
            $ pip install probabilistic2020
        
        The scripts for Probabilstic 20/20 can then be found in `Your_Python_Root_Dir/bin`. You can
        check the installation with the following:
        
        .. code-block:: bash
        
            $ which probabilistic2020
            $ probabibilistic2020 --help
        
        Local installation
        ~~~~~~~~~~~~~~~~~~
        
        Local installation is a good option if you do not have privilege to install a python package and already have the required packages.  The source files can also be manually downloaded from github at https://github.com/KarchinLab/probabilistic2020/releases.
        
        **Required packages:**
        
        * numpy
        * scipy
        * pandas>=0.17.0
        * pysam
        
        If you don't have the above required packages, you will need to install them. For the following commands to work you will need `pip <http://pip.readthedocs.org/en/latest/installing.html>`_. If you are using a system wide python, you will need to use `sudo` before the pip command. Also if you are using python 3.X then you likely will have to install pysam version >=0.9.0.
        
        .. code-block:: bash
        
            $ cd probabilstic2020
            $ pip install -r requirements.txt
        
        If you want the exact package version used for development on python 2.7, then instead use the requirements_dev.txt. Next you will need to build the Probabilistic 20/20 source files. This is can be accomplished in one command.
        
        .. code-block:: bash
        
            $ make build
        
        Once finished building you can then use the scripts in the `probabilstic2020/prob2020/console` directory. You can check the build worked by the following:
        
        .. code-block:: bash
        
            $ python prob2020/cosole/probabibilistic2020.py --help
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
