Command-line tool for simulating predictive datasets from MrBayes' output.
predsim is a simple 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 library DendroPy.
The code has been tested with Python 2.7 and 3.6.
Source repository: https://github.com/jmenglund/predsim
- Python (version 2.7 or 3.x)
- The Python library DendroPy (version 4.0 or higher)
- The command-line tool Seq-Gen
An easy way to get Python working on your computer is to install the free Anaconda distribution.
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.
predsim --help usage: predsim [-h] [-V] [-l N] [-g N] [-s N] [-n N] [-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 -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.
- Depending on your Python version, 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:
$ pytest test_predsim.py
Test coverage can be calculated with Coverage.py using the following commands:
$ coverage run -m pytest test_predsim.py $ coverage report -m predsim.py
$ pycodestyle predsim.py test_predsim.py setup.py
predsim is distributed under the MIT license.
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 and DendroPy, 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.
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|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|predsim-0.2.1-py3-none-any.whl (6.8 kB) Copy SHA256 hash SHA256||Wheel||py3||May 19, 2018|
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