seismic renumct

Purpose

seismic renumct renumbers the positions in CT (connectivity table) files. Use it when a CT file from an external source uses a different numbering scheme than your reference sequence (e.g. starts at a position other than 1), and you need the positions to match before using the file with SEISMIC-RNA.

Inputs

CT files or directories containing CT files: Passed via --ct-pos-5 FILE FIRST (see Options below). See Connectivity Table (CT): RNA secondary structures.

Outputs

Renumbered CT files. By default, written to the output directory (--out-dir). With --inplace, the original files are overwritten.

Quick example

Renumber struct.ct so that position 1 in the file corresponds to position 34 in the reference (i.e. set the 5’ position to 34):

seismic renumct --ct-pos-5 struct.ct 34

Options

--ct-pos-5 FILE N: CT file (or directory of CT files) and the 1-based 5’ position to assign. Repeat for multiple files.
--inplace/--no-inplace: Overwrite the original files (default off).

Warning

--inplace is irreversible — back up your files first.
--out-dir DIR (-o): Write renumbered files here (default ./out). Ignored when --inplace is set.

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

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