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        "author": "Markus Englund",
        "author_email": "jan.markus.englund@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
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        "description": "predsim\n=======\n\n|Build-Status| |Coverage-Status| |PyPI-Status| |License| |DOI-URI|\n\n**predsim** is a simple command-line tool for simulating predictive\ndatasets from `MrBayes' <http://mrbayes.sourceforge.net>`_ output files. \nDatasets can be simulated under the GTR+G+I substitution model or any nested \nvariant available in MrBayes (JC69, HKY85 etc.). The code is contained\nwithin a single module that can be imported using Python's import mechanism.\nThe tool uses `Seq-Gen <http://tree.bio.ed.ac.uk/software/seqgen/>`_ for\nsimulating the DNA-sequences and builds on the third-party library\n`DendroPy <http://dendropy.org>`_.\n\nThe code has been tested with Python 3.3 and 3.6.\n\nSource repository: `<https://github.com/jmenglund/predsim>`_\n\n--------------------------------\n\n.. contents:: Table of contents\n   :local:\n   :backlinks: none\n\n\nPrerequisites\n-------------\n\n* Python 3.3+\n* The Python library `DendroPy <http://dendropy.org>`_ (version 4.0 or higher)\n* The command-line tool `Seq-Gen <http://tree.bio.ed.ac.uk/software/seqgen/>`_\n\nAn easy way to get Python working on your computer is to install the free\n`Anaconda distribution <http://anaconda.com/download)>`_.\n\n\nInstallation\n------------\n\nFor most users, the easiest way is probably to install the latest version \nhosted on `PyPI <https://pypi.org/>`_:\n\n.. code-block::\n\n    $ pip install predsim\n\nThe project is hosted at `<https://github.com/jmenglund/predsim>`_ and \ncan also be installed using git:\n\n.. code-block::\n\n    $ git clone https://github.com/jmenglund/predsim.git\n    $ cd predsim\n    $ python setup.py install\n\n\nYou may consider installing predsim and its required Python packages \nwithin a virtual environment in order to avoid cluttering your system's \nPython path.\n\n\nUsage\n-----\n\n.. code-block::\n\n    $ predsim --help\n    usage: predsim [-h] [-V] [-l N] [-f #A #C #G #T] [-g N] [-s N] [-n N]\n                   [-o {nexus,phylip}] [-p FILE] [--seeds-file FILE]\n                   [--commands-file FILE] [--trees-file FILE]\n                   pfile tfile\n\n    A command-line utility that reads posterior output of MrBayes and simulates\n    predictive datasets with Seq-Gen.\n\n    positional arguments:\n      pfile                 path to a MrBayes p-file\n      tfile                 path to a MrBayes t-file\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      -V, --version         show program's version number and exit\n      -l N, --length N      sequence lenght (default: 1000)\n      -f #A #C #G #T, --freqs #A #C #G #T\n                            base frequences (overrides any base frequences in\n                            MrBayes' output)\n      -g N, --gamma-cats N  number of gamma rate categories (default: continuous)\n      -s N, --skip N        number of records (trees) to skip at the beginning of\n                            the sample (default: 0)\n      -n N, --num-records N\n                            number of records (trees) to use in the simulation\n      -o {nexus,phylip}, --out-format {nexus,phylip}\n                            output format (default: \"nexus\")\n      -p FILE, --seqgen-path FILE\n                            path to a Seq-Gen executable (default: \"seq-gen\")\n      --seeds-file FILE     path to file with seed numbers (e.g. for debugging\n                            purposes)\n      --commands-file FILE  path to output file with commands used by Seq-Gen\n      --trees-file FILE     path to output file with trees used by Seq-Gen\n\n* If base frequences are missing from MrBayes' output, these must be set manually\n  with the ``-f`` (or ``--freqs``) flag.\n* It is recommended that you use the ``--commands-file`` and ``--trees-file`` \n  flags to check the input given to Seq-Gen.\n\n\nRunning the tests\n-----------------\n\nTesting is carried out with `pytest <https://docs.pytest.org/>`_:\n\n.. code-block::\n\n    $ pytest test_predsim.py\n\nTest coverage can be calculated with `Coverage.py\n<https://coverage.readthedocs.io/>`_ using the following commands:\n\n.. code-block::\n\n    $ coverage run -m pytest test_predsim.py\n    $ coverage report -m predsim.py\n\nThe code follow style conventions in `PEP 8\n<https://www.python.org/dev/peps/pep-0008/>`_, which can be checked\nwith `pycodestyle <http://pycodestyle.pycqa.org>`_:\n\n.. code-block::\n\n    $ pycodestyle predsim.py test_predsim.py setup.py\n\n\nLicense\n-------\n\npredsim is distributed under the \n`MIT license <https://opensource.org/licenses/MIT>`_.\n\n\nCiting\n------\n\nIf you use results produced with this package in a scientific \npublication, please just mention the package name in the text and \ncite the Zenodo DOI of this project:\n\n|DOI-URI|\n\nYou can select your preferred citation style in the \"Cite as\" section\non the Zenodo page.\n\npredsim relies on other software that also should be cited. Below are \nsuggested citations for Seq-Gen and DendroPy:\n\n* Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte \n  Carlo simulation of DNA sequence evolution along phylogenetic trees. \n  Comput. Appl. Biosci. 13:235\u2013238. DOI:\n  `10.1093/bioinformatics/13.3.235 <https://doi.org/10.1093/bioinformatics/13.3.235>`_\n\n* Sukumaran J, Holder MT. 2010. DendroPy: a Python library for \n  phylogenetic computing. Bioinformatics 26:1569\u20131571. DOI:\n  `10.1093/bioinformatics/btq228 <https://doi.org/10.1093/bioinformatics/btq228>`_\n\n\nAuthor\n------\n\nMarkus Englund, `orcid.org/0000-0003-1688-7112 <http://orcid.org/0000-0003-1688-7112>`_\n\n.. |Build-Status| image:: https://travis-ci.org/jmenglund/predsim.svg?branch=master\n   :target: https://travis-ci.org/jmenglund/predsim\n.. |Coverage-Status| image:: https://codecov.io/gh/jmenglund/predsim/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/jmenglund/predsim\n.. |PyPI-Status| image:: https://img.shields.io/pypi/v/predsim.svg\n   :target: https://pypi.python.org/pypi/predsim\n.. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg\n   :target: https://raw.githubusercontent.com/jmenglund/predsim/master/LICENSE.txt\n.. |DOI-URI| image:: https://zenodo.org/badge/23107/jmenglund/predsim.svg\n   :target: https://zenodo.org/badge/latestdoi/23107/jmenglund/predsim\n\n\n",
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