Program and Scripts

Using DendroPy Interoperability Modules to Download and Align GenBank Sequences and Estimate a Maximum Likelihood Tree

Submitted by Jeet Sukumaran on

The following example shows how easy it can be to use the three interoperability modules provided by the DendroPy Phylogenetic Computing Library to download nucleotide sequences from GenBank, align them using MUSCLE, and estimate a maximum-likelihood tree using RAxML.

Pure-Python Implementation of Fisher's Exact Test for a 2x2 Contingency Table

Submitted by Jeet Sukumaran on

While Python comes with many "batteries included", many others are not. Luckily, thanks to generosity and hard work of various members of the Python community, there are a number of third-party implementations to fill in this gap. For example, Fisher's exact test is not part of the standard library.

Buffersaurus: A Vim Plugin for Searching and Indexing Across Buffers (with Context!)

Submitted by Jeet Sukumaran on

Description

Buffersaurus is a Vim plugin for searching and indexing the contents of buffers for regular expression patterns or collections of regular expression patterns. Results are displayed in separate buffer, and can be (optionally) viewed with user-specifiable lines of context (i.e., a number of lines before and/or after the line matching the search pattern) or filtered for specific patterns.

Global commands provided include (among others):

TeX-PDF : Lightweight "stay-out-of-your-way" TeX-to-PDF Development Support (in Vim)

Submitted by Jeet Sukumaran on

Description

This plugin provides support for specialized lightweight "stay-out-of-your-way" TeX-to-PDF compilation and viewing. In contrast to some of the other more comprehensive TeX/LaTeX suites, it provides nothing else but two commands, and leaves the rest of your Vim platform undisturbed, except for a few key maps to invoke the commands.

Easily Create (Clean) Compressed Tarballs of Your Git Repository

Submitted by Jeet Sukumaran on

Ideally, you could refer the whole world --- or at least, the significant portion thereof that want your code --- to your (public mirror) Git repository. But unfortunately, the whole world does not (yet) use Git ("I know it was you Fredo, I know it was you, and it breaks my heart."). Sad. Sooooo sad. But true. So the only recourse is for you to send these tortured souls an archived snapshot of your code via e-mail. I'll pause now to let you finish retching/sobbing/lamenting/venting. ... Back? Anyway, Git has a neat "archive" command that helps you create the required archive, but perhaps it does not have the most friendliest interface in the world. I've written some scripts to wrap the Git command to facilitate its use, which I share here.

Update 2011-07-07: I have re-written the original three scripts previously described here as a single script, incorporating some of the excellent suggestions that kind folks provided in the comments. Immediately below this is the new, unified, all-bells-and-whistles-included script. Simply name it something like "git-makedist", switch on its executable bit, and place it somewhere on your system path. Reasonable names, filepaths, prefixes, etc. are all provided if you do not explicitly specify them. All of which means that, in most cases, once installed, simply invoking the command "git makedist" without any options or arguments from within a Git repository "just works (tm)", resulting in a sensibly-named compressed archive of the current HEAD ready for distribution. At the same time, various flags and options allow you to fine-tune the operations, e.g. determine the compression/archive method, the path prefixes, the archive name, etc.

Update 2011-07-22, Excluding Files: Sometimes, not all files need to make it out to an archive. You can use the ".gitattributes" file to control which files get archived. Simply add the paths/names/globs of the files or directories you would like to exclude, and add a "export-ignore" after it. For example: 

.gitattributes export-ignore
.gitignore export-ignore
*.tmp export-ignore

Note that the ".gitattributes" file has to be committed for it to have an effect.

"Mayan Smoke" Vim Color Scheme

Submitted by Jeet Sukumaran on

This is "Mayan Smoke", a pleasant and ergonomic light-background color scheme, designed for long hours of coding and working. The UI elements are muted without being drab, the syntax elements are colorful without being garish, and the background is relaxing without being soporific. It is of a low-enough contrast so as not to cause eye-burn, but high-enough contrast so as not to cause eye-strain. The syntax coloration offers just a little higher resolution than most, distinguishing between class names vs.

All About Your Python(s)

Submitted by Jeet Sukumaran on

Updated 2010-04-18: Revised version of script which allows it to work when running under Python 3.x. See here for details on the byte string vs. unicode string problems when reading "stdout" or "stderr" streams of "subprocess.POpen()" under Python 3.x.

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?" or "where is the current Python's 'site-packages' directory?". Though all this information is usually one or two commands away, it can be pretty tedious jump through these hoops every time this information is required. Also, often mature systems that have gone through various systems administrators and upgrades have both legacy and current stuff scattered all over the place, and it can be a hassle trying to figure out where the site packages and other components of a particular installation of Python are located.

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