Execute Selected Lines of (Optionally) Marked-Up Python Code in a Vim Buffer

There are a number of solutions for executing Python code in your active buffer in Vim. All of these expect the buffer lines to be well-formatted Python code, with correct indentation. Many times, however, I am working on program or other documentation (in, for example reStructuredTex or Markdown format), and the code fragments that I want to execute have extra indentation or line leaders. For example, a reStructuredText buffer might look like:

Read more

Download Sequences from GenBank, Keeping Only Codons

The following script takes a space separated list of GenBank numbers as input, and then uses BioPython to download the corresponding sequences from GenBank, strips off all non-coding nucleotides, gives the sequences sensible names, and assembles them into a FASTA file. It is pretty basic, and does not do a lot of fancy error checking, and is probably a little too specific to be useful for most people. I can imagine extending it in a number of ways that would make it much more useful in a number of different contexts.

Read more

An Idiosyncratic Analogical Overview of Some Programming Languages from an Evolutionary Biologist's Perspective

R R is like a microwave oven. It is capable of handling a wide range of pre-packaged tasks, but can be frustrating or inappropriate when trying to do even simple things that are outside of its (admittedly vast) library of functions. Ever tried to make toast in a microwave? There has been a push to start using R for simulations and phylogenetic analysis, and I am actually rather ambiguous about how I feel about this.

Read more

All About Your Python(s)

Here I present a script that provides diagnostics about the current Python execution context, or the Python environment of the interpreter passed as an argument. As a Python developer, I have multiple Python versions side-by-side for testing purposes, using scripts that munge my $PATH variable to “import” and “unimport” different versions of Python as I need them. While “which python” is always available, many times I want to know things like, “what is the version of the current default Python?

Read more

Adding Test Code Coverage Analysis to a Python Project's Setup Command

I recently integrated unit test code coverage analysis (using coverage) as a setuptools command extension into the DendroPy phylogenetic computing library, and thought that I would share how this was done. Providing the Command Extension The first step is to provide the command functionality in a class that derives from “setuptools.Command” in a separate module of the package, which, in my case, was called “coverage_analysis.py”, located in the “test/support” subdirectory of the DendroPy package

Read more