jupiter

Generate "Jupiter" plots for circular genomes

Description

Python scripts to generate plots from ViennaRNA output.

Written in "pidgin" python with no external dependencies (no third-party libaries), the idea here is that novice programmers will be able to understand enough of the code to hack it to suite their own needs.

Generating a plot is a two-step process. Input is a ViennaRNA postscript (ps) file. The first step converts ps to TSV, the second step converts TSV to SVG.

jupiter_ps2tsv.py

python3 jupiter_ps2tsv.py vienna.ps > vienna.tsv

jupiter_tsv2svg.py

python3 jupiter_tsv2svg.py vienna.tsv [configfile] > vienna.svg

TSV file format

TSV fields are:

1. i Base postion 0, 1 ... (L-1) where L is genome length.
2. x x coordinate.
3. y y coordinate.
4. S S array from ps file (Score?).
5. j Position of paired base, or period '.' if unpaired.

The x,y coordinates are position of a base on a circle, they are re-scaled to range from zero to one so the circle diameter is one and the circle center is x=0.5, y=0.5.

Config file format

The optional configfile is used to set rendering style. Format is tab-separated text where the first field is the parameter name and subsequent fields (usually just one) gives the value(s). Parameters are:

line Line width, floating point, default 1.
bend Sets "bendiness" of the arcs, default 1.
hb Bezier handle offset, default 1.
colors heatmap colors, default 0x0000ff 0x00ff00 0xffff00 0xff0000

All parameters are optional and may be specified in any order.

Example config file:

line 0.5
bend 2.2
colors 0x000000 0x500000 0x900000 0xff0000