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Drawing sequence logos
A very simple script to do a simple but tedious task.
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.
Usage is:
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.
Requirements
- 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.
