Software
Subversion repository
I have written a variety of programs to handle everyday tasks such as batch file renaming and selecting rows from a delimited file, to bioinformatic scripts. The majority of code is Python, with some scabs of Perl, all of which is available to use or peruse. Please give credit where it’s due, and apologies for the many imperfections…
- Download the code
- Or, for the latest versions, tap into my subversion repository:
svn co svn://dfsimola.com/svn/simolacode/trunk simolacode
calcify.py, server-based generation of static blosxom pages
Although blosxom provides a built-in method of static page generation, sadly it generates bunk when you use any of a variety of available plugins. As this site makes use of some of these plugins, I needed a new way of generating static pages. Since actually viewing the pages over the internet (or localhost) works just fine, I figured I would just recapitulate my blosxom data directory structure through calls to curl.
calcify.py takes in the path to your blosxom data directory, and curls each .txt file, saving the resultant html file. You can either save these html files in place, or to a separate folder (i.e. just like blosxom static generation). In addition you can generate pages via a localhost server for use over the internet by specifying a new domain name which is used to replace localhost instances in all pages.
Entitymapping
Very simple Blosxom plugin to convert commonly used symbols (i.e. many of which are part of an ASCII 8-bit encoding) into HTML entites that work on an ASCII 7-bit encoding. I really just wanted to be able to type option-m and option-0 on my Mac to get uncorrupted µ’s and °’s respectively.
Yeast Population Genomics Data base
After Sanger released assembled genomes for several dozen isolates of 2 budding yeast species, I worked on their genome annotations to do a cursory evolutionary study of gene structure within and between species. Though the manuscript remains unpublished, there is a live web site hosted at Penn that provides the data and statistics for general use.
