seismic draw

Purpose

seismic draw renders predicted RNA secondary structures as 2D diagrams, coloring each base by its mutation rate reactivity. It uses RNArtistCore to generate publication-quality SVG images.

Requires RNArtistCore (installed automatically on first run unless --no-update-rnartistcore is set).

Inputs

Fold CT files or fold output directories: One or more CT files or fold-report.json files produced by seismic fold. See Specify Input Files.
Table CSV files (optional): Per-position mutation rate tables to color the bases. If omitted, bases are drawn without color.

Outputs

All outputs go into {out}/{sample}/draw/{ref}/{reg}/.

{profile}-{n}.svg: SVG diagram of structure n of a profile, e.g. {reg}__average-0.svg (one file per drawn structure).
{profile}-{n}.png: PNG diagram (only if --draw-png is set).

Quick example

Draw all predicted structures for sample-1:

seismic draw out/sample-1/fold/ref-1

Options

Structure selection

--struct-num N: Draw structure number N (0-indexed); -1 for all structures. Default: draw the structure with the best AUC-ROC.

Appearance

--color/--no-color: Color bases by their reactivity (default on).
--draw-svg/--no-draw-svg: Output SVG files (default on).
--draw-png/--no-draw-png: Output PNG files (default off).

Maintenance

--update-rnartistcore/--no-update-rnartistcore: Check for and install updates to RNArtistCore (default off).

Performance

--num-cpus N — multiprocessing; see Parallelize Tasks. --force — overwrite existing outputs.

The auto-generated Command Line Reference lists every option with its current default.