Metadata-Version: 1.1
Name: predsim
Version: 0.1.1
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| |PyPI-Status| |License| |DOI-URI|
        
        ``predsim`` is a 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 script uses 
        `Seq-Gen <http://tree.bio.ed.ac.uk/software/seqgen/>`_ for 
        simulating the DNA-sequences and builds on the third-party libraries 
        `DendroPy <http://dendropy.org>`_ and `pandas <http://pandas.pydata.org>`_.
        
        The code has been tested with Python 2.7, 3.3, 3.4 and 3.5.
        
        Source repository: `<https://github.com/jmenglund/predsim>`_
        
        --------------------------------
        
        .. contents:: Table of contents
           :backlinks: top
           :local:
        
        
        Requirements
        ------------
        
        `Seq-Gen <http://tree.bio.ed.ac.uk/software/seqgen/>`_ must be installed on
        your system.
        
        
        Installation
        ------------
        
        For most users, the easiest way is probably to install the latest version 
        hosted on `PyPI <https://pypi.python.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. See for example the environment management system 
        `conda <http://conda.pydata.org>`_ or the package 
        `virtualenv <https://virtualenv.pypa.io/en/latest/>`_.
        
        
        Usage
        -----
        
        .. code-block::
            
            $ predsim --help
            usage: predsim [-h] [-V] [-l INT] [-g INT] [-c FILE] [-s INT] [-p 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 INT, --length INT  sequence lenght (default: 1000)
              -g INT, --gamma-cats INT
                                    number of gamma rate categories (default: continuous)
              -c FILE, --commands-file FILE
                                    path to output file with used Seq-Gen commands
              -s INT, --skip INT    number of records (trees) to skip at the beginning of
                                    the sample (default: 0)
              -p FILE, --seqgen-path FILE
                                    path to a Seq-Gen executable (default: "seq-gen")
        
        
        * It is strongly recommended that you use the ``-c FILE`` option to check the 
          commands run by Seq-Gen.
        
        * Depending on your Python version, you might need to specify the full path to 
          your Seq-Gen executable with the ``-p FILE`` option.
        
        
        Running tests
        -------------
        
        Testing is carried out with `pytest <http://pytest.org>`_. Here is an 
        example on how to run the test suite and generating a coverage report:
        
        .. code-block::
        
            $ cd predsim
            $ pip install pytest pytest-cov pytest-pep8
            $ py.test -v --cov-report term-missing --cov predsim.py --pep8
        
        
        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 a citation style from the dropdown menu 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, DendroPy and pandas, 
        respectively:
        
        * 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.
        
        * McKinney W. 2010. Data structures for statistical computing in python.
          *In* Proceedings of the 9th Python in Science Conference 
          (van der Walt S, Millman J, editors), pages 51–56.
        
        
        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
        .. |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,Seq-Gen,DendroPy
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 :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
