seismic ct2db

Purpose

seismic ct2db converts RNA secondary structure files from CT (connectivity table) format to dot-bracket format. Use it when a downstream tool requires dot-bracket notation.

Inputs

CT files: One or more .ct files. See Connectivity Table (CT): RNA secondary structures.

Outputs

Dot-bracket files (.db) written alongside the input CT files. See Dot-bracket (DB): RNA secondary structures.

Quick example

Convert a CT file to dot-bracket:

seismic ct2db struct.ct

Options

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

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

See also

seismic db2ct — the reverse conversion
Connectivity Table (CT): RNA secondary structures, Dot-bracket (DB): RNA secondary structures
seismic renumct — renumber positions in CT files