Skip to content

Rename Seqs

Summary

Rename sequences in a FASTA file with consistent IDs (supports numbering or hashing, appending attributes like GC and length).

Description

This tool renames sequences in a FASTA file using either sequential numbers or hashes, and generates a lookup table mapping old IDs to new IDs. Optionally includes sequence statistics (length, GC content).

Usage

rolypoly rename-seqs [OPTIONS]

Options

  • -i, --input: Input FASTA file (type: TEXT; required; default: Sentinel.UNSET)
  • -o, --output: Output FASTA file (type: TEXT; required; default: Sentinel.UNSET)
  • -m, --mapping: Output mapping file (TSV) (type: TEXT; required; default: Sentinel.UNSET)
  • -p, --prefix: Prefix for new sequence IDs (type: TEXT; default: CID)
  • --hash, --no-hash: Use hash instead of a padded running number for IDs (type: BOOLEAN; default: False)
  • --stats, --no-stats: Include sequence statistics in mapping file (length, GC content) (type: BOOLEAN; default: True)