Showing posts from October 11, 2009


I've been trying in 2009 to write less throw-away code. I'm not sure how successful I've been at that, but at least I'm writing more code that I keep around.
Previously, I stuck anything of at least marginal quality and re-usability into my google code project bpbio. As of yesterday, I've moved a lot of stuff from there to bitbucket. "Biostuff" is where I'll put modules that are well documented and tested in hopes that using a distributed VCS and a project that doesn't contain my initials will foster any contribution. Currently, all the modules on bitbucket are also on pypi.

pyfasta provides pythonic access fasta sequence files. Previously, it had been a part of genedex (which I've stopped supporting since @hobu has done so much good work on Rtree that genedex is now pretty much obsolete) but it's been pulled out and simplified and improved. Check out the docs on pypi.

nwalign is a command-line or python interface to the Needleman-Wunsch glo…