This is a repository of example scripts that demonstrate how to use dendropy 4 to accomplish some basic tasks. The goal is for this to host some small, self-contained scripts that demonstrate best practices, but which are too arcane to belong inside DendroPy itself.

Code should run on python 2.7 and python 3 Each script should be (somewhat) useful in and of itself, and we should try to limit dependencies as much as possible.

The handling of arg-parsing should be done in the if __name__ == '__main__': block of code.

If there are additional user-interface steps (e.g. creation of intermediate directories, or translation of exceptions into sys.exit calls) they should be done in a _main function.

As much as possible, the _main function should delegate the work to be done to a function with a name that corresponds with the script name.

Adhering to these conventions will make it easier for users to navigate the examples (because of the consistency) and allow them to piece together larger pipelines (by calling the same business logic functions that _main calls). If you think that your script might be generally useful, you may want to add it to the list of imports in dendrobites/__init__.py so that client code can easily import it.

If you are interested in contributing scripts to DendroBites, feel free to email Mark or Jeet.

As well as depending on DendroPy, DendroBites also borrows code from it. DendroPy is written by Jeet Sukumaran and Mark T. Holder.