seismic cleanfa

Purpose

seismic cleanfa fixes FASTA files that are incompatible with SEISMIC-RNA. Common issues from databases like NCBI and Gencode include metadata in header lines and non-standard characters in sequences. It trims headers to valid path characters, uppercases sequence bases, replaces ambiguous IUPAC codes with N, and converts U``↔``T as needed.

Inputs

FASTA files: One or more FASTA files to clean.

Outputs

Cleaned FASTA files with the same names as the inputs, written to the output directory (default ./out).

Quick example

Clean a reference FASTA:

seismic cleanfa refs.fa

Output goes to out/refs.fa. Specify a different directory with -o:

seismic cleanfa -o clean refs.fa

Options

--inplace/--no-inplace: Overwrite the original files instead of writing to --out-dir (default off).

Warning

--inplace is irreversible — back up your files first.
--out-dir DIR (-o): Write cleaned 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.

Common unexpected results

Line contains sequence characters other than whitespace or IUPAC codes: The sequence has characters that cannot be interpreted automatically. Remove them manually and rerun. The error message names the affected line(s).