Metadata-Version: 1.1
Name: MGLEX
Version: 0.2.1
Summary: MGLEX - MetaGenome Likelihood EXtractor
Home-page: https://github.com/fungs/mglex
Author: Johannes Dröge
Author-email: code@fungs.de
License: GNU General Public License, version 3 (GPL-3.0)
Description: ===============================
        MGLEX
        ===============================
        
        This Python Package provides a probabilistic model to classify nucleotide
        sequences in metagenome samples. It was developed as a framework to help
        researchers to reconstruct individual genomes from such datasets using custom
        workflows and to give developers the possibility to integrate the model into
        their programs.
        
        * Free software: GPLv3 license
        * Source code: https://github.com/fungs/mglex
        * Documentation: https://mglex.readthedocs.io
        
        Features
        --------
        
        * Integrates nucleotide composition, multi-sample coverage
          and taxonomic annotation
        * Learns a model in linear time with respect to the number of input sequences
        * Classifies novel sequences in linear time
        * Calculates likelihood and p-values
        * Calculates probabilistic distances between genome bins
        
        Dependencies
        ------------
        
        MGLEX is a Python 3 package, it **does not run with Python 2 versions**. It depends on
        
        * NumPy
        * SciPy (for few functions)
        * docopt
        
        Installation
        ------------
        
        Install dependencies with Debian/Ubuntu & Python-Virtualenv
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        We show how to install MLGEX under Debian and Ubuntu, but other platforms are similar.
        
        You can simply install the requirements as system packages.
        
        .. code-block:: sh
        
           sudo apt install python3 python3-numpy python3-scipy
        
        We recommend to create a `Python virtual installation enviroment <https://docs.python.org/3/library/venv.html>`_ for MGLEX. In order to do so, install the venv package for your Python version (e.g. the Debian package python3.4-venv), if not included (or use `virtualenv <https://pypi.python.org/pypi>`_). The following command will make use of the installed system packages.
        
        .. code-block:: sh
        
           python3 -m venv --system-site-packages mglex-env
           source mglex-env/bin/activate
        
        Install dependencies with Conda
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Similarly, you can use Anaconda or Conda to prepare an environment with the dependencies and activate it.
        
        .. code-block:: sh
        
           conda create -n mglex-env -c conda-forge numpy scipy docopt python=3
           source activate mglex-env
        
        Install MGLEX Python package 
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        MGLEX is deposited on the `Python Package Index <https://pypi.python.org/pypi>`_ and we recommend to install it via `pip <https://docs.python.org/3/installing/>`_.
        
        .. code-block:: sh
        
           python -m pip install mglex
        
        Credits
        ---------
        
        This package was created using NumPy by Johannes Dröge at the Computational
        Biology of Infection Research Group at the Helmholtz Centre for Infection
        Research, Braunschweig, Germany.
        
        Please cite:
        
        Dröge J, Schönhuth A, McHardy AC. (2017)
        A probabilistic model to recover individual genomes from metagenomes.
        PeerJ Computer Science 3:e117 https://doi.org/10.7717/peerj-cs.117
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Operating System :: POSIX :: Linux
