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Annotate

Summary

Run combined RNA + protein annotation on nucleotide viral sequences.

Description

This command orchestrates annotate-rna and annotate-prot into a single workflow and writes results into rna_annotation/ and protein_annotation/ subdirectories under the selected output path.

Use --skip-steps to disable specific stages and --override-parameters to forward JSON overrides to sub-tools.

Usage

rolypoly annotate [OPTIONS]

Options

  • -i, --input: Input nucleotide sequence file (fasta, fna, fa, or faa) (type: PATH; required; default: Sentinel.UNSET)
  • -o, --output: Output file location. (type: TEXT; default: rolypoly_annotation)
  • --override-parameters: JSON-like string of parameters to override. Example: --override-parameters '{"RNAfold": {"temperature": 37}, "ORFfinder": {"minimum_length": 150}}' (type: TEXT; default: {})
  • --skip-steps: Comma-separated list of steps to skip. Example: --skip-steps RNA_annotation,protein_annotation or --skip-steps IRESfinder,RNAMotif or --skip-steps ORFfinder,hmmsearch (type: TEXT; default: ``)
  • --secondary-structure-tool: Tool for secondary structure prediction (type: CHOICE; default: LinearFold)
  • --ires-tool: Tool for IRES identification (type: CHOICE; default: IRESfinder)
  • --trna-tool: Tool for tRNA identification. ARAGORN NOT FULLY SUPPORTED YET (type: CHOICE; default: tRNAscan-SE)
  • --gene-prediction-tool: Tool for gene prediction (type: CHOICE; default: pyrodigal)
  • --domain-db: Database for domain detection (type: CHOICE; default: Pfam)
  • --custom-domain-db: Path to a custom domain database in HMM format (for use with --domain-db custom) (type: TEXT; default: ``)
  • --min-orf-length: Minimum ORF length for gene prediction (type: INTEGER; default: 30)
  • --search-tool: Tool/command for protein domain detection. hmmer commands are via pyhmmer bindings. (type: CHOICE; default: hmmsearch)
  • --html, --no-html: Write an interactive HTML genome-map report (genome_maps.html) combining the protein and RNA annotations. Use --no-html when calling from roll, which writes the report itself at the end. (type: BOOLEAN; default: True)
  • -t, --threads: Number of worker threads. (type: INTEGER RANGE; default: 1)
  • -M, --memory: Memory limit, for example 8g. (type: MEMORY; default: 8g)
  • -k, --keep-tmp: Keep temporary files. (type: BOOLEAN; default: False)
  • -tmp, --temp-dir: Temporary working directory. (type: DIRECTORY)
  • -g, --log-file: Path to the log file. (type: FILE; default: rolypoly.log)