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