{ "info": { "author": "Johannes Dr\u00f6ge", "author_email": "code@fungs.de", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: POSIX :: Linux", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "===============================\nMGLEX\n===============================\n\nThis Python Package provides a probabilistic model to classify nucleotide\nsequences in metagenome samples. It was developed as a framework to help\nresearchers to reconstruct individual genomes from such datasets using custom\nworkflows and to give developers the possibility to integrate the model into\ntheir programs.\n\n* Free software: GPLv3 license\n* Source code: https://github.com/fungs/mglex\n* Documentation: https://mglex.readthedocs.io\n\nFeatures\n--------\n\n* Integrates nucleotide composition, multi-sample coverage\n and taxonomic annotation\n* Learns a model in linear time with respect to the number of input sequences\n* Classifies novel sequences in linear time\n* Calculates likelihood and p-values\n* Calculates probabilistic distances between genome bins\n\nDependencies\n------------\n\nMGLEX is a Python 3 package, it **does not run with Python 2 versions**. It depends on\n\n* NumPy\n* SciPy (for few functions)\n* docopt\n\nInstallation\n------------\n\nInstall dependencies with Debian/Ubuntu & Python-Virtualenv\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nWe show how to install MLGEX under Debian and Ubuntu, but other platforms are similar.\n\nYou can simply install the requirements as system packages.\n\n.. code-block:: sh\n\n sudo apt install python3 python3-numpy python3-scipy\n\nWe recommend to create a `Python virtual installation enviroment `_ 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 `_). The following command will make use of the installed system packages.\n\n.. code-block:: sh\n\n python3 -m venv --system-site-packages mglex-env\n source mglex-env/bin/activate\n\nInstall dependencies with Conda\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nSimilarly, you can use Anaconda or Conda to prepare an environment with the dependencies and activate it.\n\n.. code-block:: sh\n\n conda create -n mglex-env -c conda-forge numpy scipy docopt python=3\n source activate mglex-env\n\nInstall MGLEX Python package \n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nMGLEX is deposited on the `Python Package Index `_ and we recommend to install it via `pip `_.\n\n.. code-block:: sh\n\n python -m pip install mglex\n\nCredits\n---------\n\nThis package was created using NumPy by Johannes Dr\u00f6ge at the Computational\nBiology of Infection Research Group at the Helmholtz Centre for Infection\nResearch, Braunschweig, Germany.\n\nPlease cite:\n\nDr\u00f6ge J, Sch\u00f6nhuth A, McHardy AC. 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