Metadata-Version: 1.1
Name: predsim
Version: 0.4.0
Summary: Command-line tool for simulating predictive datasets from MrBayes' output.
Home-page: https://github.com/jmenglund/predsim
Author: Markus Englund
Author-email: jan.markus.englund@gmail.com
License: MIT
Description: predsim
        =======
        
        |Build-Status| |Coverage-Status| |PyPI-Status| |License| |DOI-URI|
        
        **predsim** is a simple command-line tool for simulating predictive
        datasets from `MrBayes <http://mrbayes.sourceforge.net>`_ output files. 
        Datasets can be simulated under the GTR+G+I substitution model or any nested 
        variant available in MrBayes (JC69, HKY85 etc.). The code is contained
        within a single module that can also be imported using Python's import
        mechanism. It uses `Seq-Gen <http://tree.bio.ed.ac.uk/software/seqgen/>`_
        for simulating the DNA-sequences and builds on the third-party library
        `DendroPy <http://dendropy.org>`_.
        
        The code has been tested with Python 2.7 and 3.6.
        
        Source repository: `<https://github.com/jmenglund/predsim>`_
        
        --------------------------------
        
        .. contents:: Table of contents
           :local:
           :backlinks: none
        
        
        Prerequisites
        -------------
        
        * Python (version 2.7 or 3.x)
        * The Python library `DendroPy <http://dendropy.org>`_ (version 4.0 or higher)
        * The command-line tool `Seq-Gen <http://tree.bio.ed.ac.uk/software/seqgen/>`_
        
        An easy way to get Python working on your computer is to install the free
        `Anaconda distribution <http://anaconda.com/download)>`_.
        
        
        Installation
        ------------
        
        For most users, the easiest way is probably to install the latest version 
        hosted on `PyPI <https://pypi.org/>`_:
        
        .. code-block::
        
            $ pip install predsim
        
        The project is hosted at `<https://github.com/jmenglund/predsim>` and 
        can also be installed using git:
        
        .. code-block::
        
            $ git clone https://github.com/jmenglund/predsim.git
            $ cd predsim
            $ python setup.py install
        
        
        You may consider installing predsim and its required Python packages 
        within a virtual environment in order to avoid cluttering your system's 
        Python path.
        
        
        Usage
        -----
        
        .. code-block::
            
            $ predsim --help
            usage: predsim [-h] [-V] [-l N] [-g N] [-s N] [-n N] [-o {nexus,phylip}]
                           [-p FILE] [--seeds-file FILE] [--commands-file FILE]
                           pfile tfile [outfile]
        
            A command-line utility that reads posterior output of MrBayes and simulates
            predictive datasets with Seq-Gen.
        
            positional arguments:
              pfile                 path to a MrBayes p-file
              tfile                 path to a MrBayes t-file
              outfile               path to output file (default: <stdout>)
        
            optional arguments:
              -h, --help            show this help message and exit
              -V, --version         show program's version number and exit
              -l N, --length N      sequence lenght (default: 1000)
              -g N, --gamma-cats N  number of gamma rate categories (default: continuous)
              -s N, --skip N        number of records (trees) to skip at the beginning of
                                    the sample (default: 0)
              -n N, --num-records N
                                    number of records (trees) to use in the simulation
              -o {nexus,phylip}, --output-format {nexus,phylip}
                                    output format (default: "nexus")
              -p FILE, --seqgen-path FILE
                                    path to a Seq-Gen executable (default: "seq-gen")
              --seeds-file FILE     path to file with seed numbers to pass to Seq-Gen
              --commands-file FILE  path to output file with used Seq-Gen commands
        
        
        * It is strongly recommended that you use the ``--commands-file`` option to
          check the commands run by Seq-Gen.
        
        * If you have Python version > 3.4, you may need to specify the full path to 
          your Seq-Gen executable by using the ``-p`` option.
        
        
        Running the tests
        -----------------
        
        Testing is carried out with `pytest <https://docs.pytest.org/>`_:
        
        .. code-block::
        
            $ pytest test_predsim.py
        
        Test coverage can be calculated with `Coverage.py
        <https://coverage.readthedocs.io/>`_ using the following commands:
        
        .. code-block::
        
            $ coverage run -m pytest test_predsim.py
            $ coverage report -m predsim.py
        
        The code follow style conventions in `PEP8
        <https://www.python.org/dev/peps/pep-0008/>`_, which can be checked
        with `pycodestyle <http://pycodestyle.pycqa.org>`_:
        
        .. code-block::
        
            $ pycodestyle predsim.py test_predsim.py setup.py
        
        
        License
        -------
        
        ``predsim`` is distributed under the 
        `MIT license <https://opensource.org/licenses/MIT>`_.
        
        
        Citing
        ------
        
        If you use results produced with this package in a scientific 
        publication, please just mention the package name in the text and 
        cite the Zenodo DOI of this project:
        
        |DOI-URI|
        
        You can select your preferred citation style in the "Cite as" section
        on the Zenodo page.
        
        predsim relies on other software that also should be cited. Below are 
        suggested citations for Seq-Gen and DendroPy:
        
        * Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte 
          Carlo simulation of DNA sequence evolution along phylogenetic trees. 
          Comput. Appl. Biosci. 13:235–238.
        
        * Sukumaran J, Holder MT. 2010. DendroPy: a Python library for 
          phylogenetic computing. Bioinformatics 26:1569–1571.
        
        
        Author
        ------
        
        Markus Englund, `orcid.org/0000-0003-1688-7112 <http://orcid.org/0000-0003-1688-7112>`_
        
        .. |Build-Status| image:: https://travis-ci.org/jmenglund/predsim.svg?branch=master
           :target: https://travis-ci.org/jmenglund/predsim
        .. |Coverage-Status| image:: https://codecov.io/gh/jmenglund/predsim/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/jmenglund/predsim
        .. |PyPI-Status| image:: https://img.shields.io/pypi/v/predsim.svg
           :target: https://pypi.python.org/pypi/predsim
        .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg
           :target: https://raw.githubusercontent.com/jmenglund/predsim/master/LICENSE.txt
        .. |DOI-URI| image:: https://zenodo.org/badge/23107/jmenglund/predsim.svg
           :target: https://zenodo.org/badge/latestdoi/23107/jmenglund/predsim
        
Keywords: simulation,predictive,Seq-Gen,DendroPy,MrBayes,phylogenetics,dna-sequences,Bayesian
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
