This script generates secondary structure diagrams for nucleic acids.
The default behavior is to output the secondary structure visualization to both svg and png. The png requires Inkscape, whose directory must be set by environmental variable INKSCAPEDIR.
An input file is used to specify the sequence, secondary structure, and coloring of the desired drawing. The format is as follows
filename # image will be written to filename.svg
GTGANNNNNTCAC # nucleic acid sequence
((((.....)))) # nucleic acid secondary structure in dot-bracket notation
rrrrbbbbbgggg # optional: coloring of each base (e.g. r for red, g for green, b for blue)
Multiple sequences can be specified in one file as in example_input.txt.
The draw script can be run with
python draw_all.py example_input.txt
