For parentage/sibship inference, I've started using Colony2 and MasterBayes in place of the venerable Cervus. However, one (of two*) things that is annoying about Colony2 are the scripts for running the program that are available on "alternative" operating systems (e.g. not Windows). These scripts are provided as part of the rcolony package.

Because the script to run colony through R (aka run.colony()) was causing me problems and because I'd rather do pretty much anything than hack on R code, I wrote some Python code to accomplish a function similar to run.colony() but that operates outside of R. Here goes:

* The second thing that can be a downer when using Colony on alternative operating systems is the formatting of the input file. I've got something in the works, there, too... it's just not at all on the front burner