TL;DR: Just look at the Gist. Summary: Act I, in which I try and fail. Act II, in which I think I succeed but actually failed without knowing it till I tried to use it. Act III, in which I return to my beginning, ponder the universe, dive deep into the depths of the abyss, and come back with the magic bean that makes everything work.
It is better than a nightmare from which you cannot wake up … Install Homebrew: $ ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)" Find problems and fix them (typically resulting from Homebrew becoming very stroppy if it does not have exclusive access to “/usr/local”): $ brew doctor VERY IMPORTANT NOTE: Make ABSOLUTELY sure that the DYLD_LIBRARY_PATH environmental variable is NOT set. Having this set will cause all sorts of problems as conflicts arise between libraries that homebrew installs that some of your other packages need (e.
All the basic examples for Python’s timeit module show strings being executed. This lead to, in my opinion, somewhat convoluted code such as: #! /usr/bin/env python import timeit def f(): pass if __name__ == "__main__": timer = timeit.Timer("__main__.f()", "import __main__") result = timer.repeat(repeat=100, number=100000) print("".format(min(result))) For some reason, the fact that you can call a function directly is only (again, in my opinion) obscurely documented. But this makes things so much cleaner:
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. The automatic label composition option of the DendroPy genbank module creates practical taxon labels out the original data. We also pass in additional arguments to RAxML to request that the tree search be carried out 250 times (['-N', '250']).
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. 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.
The pyPDF package provides really nice facilities for PDF document manipulation. Here is a simple application script to extract a specified subset of pages from a PDF file. [gist id=2189062 file=extract-pdf-pages.py]
UPDATE Nov 7, 2009: Better parsing of traceback. UPDATE Nov 4, 2009: Now passing a “-b” flag to the script opens the parsed stack frame references in a BBEdit results browser, inspired by an AppleScript script by Marc Liyanage. When things go wrong in a Python script, the interpreter dumps a stack trace, which looks something like this: $ python y.py Calling f1 ... Traceback (most recent call last): File "y.
Given a list of strings, how would you iterpolate a multi-character string in front of each element? For example, given: >>> k = ['the quick', 'brown fox', 'jumps over', 'the lazy', 'dog'] The objective is to get: ['-c', 'the quick', '-c', 'brown fox', '-c', 'jumps over', '-c', 'the lazy', '-c', 'dog'] Of course, the naive solution would be to compose a new list by iterate over the original list: >>> result =  >>> for i in k: .
The DendroPy Phylogenetic Computing Library includes native infrastructure for phylogenetic sequence simulation on DendroPy trees under the HKY model. Being pure-Python, however, it is a little slow. If Seq-Gen is installed on your system, though, you can take advantage of a lightweight Seq-Gen wrapper added to the latest revision under the interop subpackage: dendropy.interop.seqgen. Documentation is lagging, but the following examples should be enough to get started, and the class is simple and straightforward enough so that all options should be pretty much self-documented.
The following is an example of how to use the “pkg_resources” module (provided by the setuptools project) to compose a list of all available modules in a Python package. #! /usr/bin/env python import sys try: import pkg_resources except ImportError: sys.stderr.write("'pkg_resources' could not be imported: setuptools installation required\n") sys.exit(1) def list_package_modules(package_name): """ Returns list of module names for package `package_name`. """ try: contents = pkg_resources.resource_listdir(package_name, "") except ImportError: return  module_names =  for entry in contents: if pkg_resources.