predsim 0.1.0

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 of its nested variants 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

• 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.

Author

Markus Englund, orcid.org/0000-0003-1688-7112