Drawing sequence logos
Sequence logos are a common way of representing SNPs and diversity in groups of sequences. This script automates the task. It's a bit rough around the edges and serves mainly as a base for further hacking.
drawlogo.rb [options] FILE1 [FILE2 ...]
where options are:
-h, --help Display this screen --columns INT How many sites to draw in every row --relative-cell-height FLOAT How high to make a site relative to its width --palette STR Which palette to use --add-to-palette STR Add these colors to the palette --format STR Save output in this format --save STR Name output files according this template -o, --overwrite Overwrite pre-existing files
The input is a CSV file with one row for each different residue at each site, of the form:
<site index>, <residue>, <proportion>
The output is an image file, by default a PNG, although any format supported by RMagick is possible. Caveat: SVG output is pathological, due to Rmagick's poor support of the format.
- Ruby v1.8.x. 1.9.x will work but require a simple change in the CSV reading code, thanks to Ruby changing the way the CSV standard library works. (Thanks guys!)
- The RMagick library.