This code was used to generate the results reported in Kremer et al. [1]. That publication describes the operation of this software and the paraters used by it.
The code runs with python 2.7.12. Other versions of python may or may not work. In particular, any version of python 3 will not work due to the format of the print statements (and possible a few other python 2, python 3 differences).
You can run any of the experiments from the original paper from the command line by chaning to the experiments directory:
e.g. cd PaperExperiments/XHExp001
And then, running the TESim.py python script from within the experiment's directory.
e.g. python2.7 ../../TEWorldCodeV2/TESim.py > expG.001.log
This will re-run the experiment with the same parameters, but with a different random seed. It will over-write the log file and the state-0000000.gz file. It will also generate a trace.csv file, a *.pyc file, and subsequent state- files.
You can also re-run the experiment with the same random seed by changing the value of saved in the parameters.py file to be "state-0000000.gz" (assuming you didn't just over-write that file by running without modifying the saved variable).
The following file will be generated by this process:
trace.csv - comma separated varialbe file tracing a number of variables on a per cycle basis (you will need to read the source code to understand what each variable means)
[1] Kremer SC, Linquist S, Saylor B, Elliot TA, Gregory TR, Cottenie K. 2020. Transposable element persistence via potential genome-level ecosystem engineering. Under review.