predsim 0.1.1

Command-line tool for simulating predictive datasets from MrBayes' output.

predsim is a command-line tool for simulating predictive datasets from MrBayes 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 for simulating the DNA-sequences and builds on the third-party libraries DendroPy and pandas.

The code has been tested with Python 2.7, 3.3, 3.4 and 3.5.

Source repository: https://github.com/jmenglund/predsim

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Table of contents

• Requirements

• Installation

• Usage

• Running tests

• License

• Citing

• Author

Requirements

Seq-Gen must be installed on your system.

Installation

For most users, the easiest way is probably to install the latest version hosted on PyPI:

$ pip install predsim

The project is hosted at https://github.com/jmenglund/predsim and can also be installed using git:

$ 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 or the package virtualenv.

Usage

$ 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. Here is an example on how to run the test suite and generating a coverage report:

$ 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.

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:

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