cdskit label

cdskit label cleans, truncates, or uniquifies FASTA/sequence record IDs. The sequence contents and record order are preserved.

Example

cdskit label \
  --seq_file input.fasta \
  --out_file labeled.fasta \
  --replace_chars " !|/--_" \
  --clip_len 60 \
  --unique yes

--replace_chars FROM--TO replaces every character in FROM with the single character TO. In the example, spaces, !, |, and / become _. Quote the value because shells treat several of these characters specially.

Operations run in this order:

1. character replacement;
2. clipping to --clip_len when it is greater than zero;
3. duplicate resolution when --unique yes.

Duplicate IDs receive _1, _2, and subsequent suffixes. Because clipping can create new duplicates, enable --unique yes when using --clip_len on IDs that may share a prefix.

Key options

• --replace_chars FROM--TO: Character replacement rule; empty by default.
• --clip_len INT: Maximum ID length; 0 disables clipping.
• --unique yes|no: Add suffixes to duplicate IDs; default no.
• --seq_type dna|protein|auto: Expected input type; default auto.

Label editing runs serially and has no --threads option.

Counts of changed, clipped, and duplicate IDs are written to standard error.

Citation

No separate method paper is designated for this utility. Report the CDSKIT version, command and options; see citing CDSKIT.