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Annotate Rna

Summary

Annotate RNA structural features and motifs on viral nucleotide inputs.

Description

The default pipeline runs secondary-structure prediction, ribozyme/CM search, and tRNA detection, while optional modules can add IRES and motif analyses depending on selected tools and skip settings.

Use `--skip-steps` to disable modules and `--override-parameters` to pass
tool-specific tuning values for individual stages.

Usage

rolypoly annotate-rna [OPTIONS]

Options

  • -i, --input: Input nucleotide sequence file (fasta, fna, fa, or faa) (type: PATH; required; default: Sentinel.UNSET)
  • -o, --output-dir: Output directory path (type: TEXT; default: ./annotate_RNA_output)
  • -t, --threads: Number of threads (type: INTEGER; default: 1)
  • -g, --log-file: Path to log file (type: TEXT; default: ./annotate_RNA_logfile.txt)
  • -l, --log-level: Log level (type: CHOICE; default: INFO)
  • -M, --memory: Memory in GB. Example: -M 8gb (type: TEXT; default: 4gb)
  • -op, --override_parameters, --override-parameters: JSON-like string of parameters to override. Example: --override-parameters '{"RNAfold": {"temperature": 37}, "cmscan": {"E": 1e-5}}' (type: TEXT; default: {})
  • --skip-steps: Comma-separated list of steps to skip. Example: --skip-steps RNAfold,cmsearch (type: TEXT; default: ``)
  • --secondary-structure-tool: Tool for secondary structure prediction. LinearFold is faster but less configurable. (type: CHOICE; default: LinearFold)
  • --ires-tool: Tool for IRES identification (type: CHOICE; default: IRESfinder)
  • --trna-tool: Tool for tRNA identification (type: CHOICE; default: tRNAscan-SE)
  • --rnamotif-tool: Tool for RNAmotif identification (type: CHOICE; default: RNAMotif)
  • --cm-db: Database for cmscan (type: CHOICE; default: Rfam)
  • --custom-cm-db: Path to a custom cm database in nhmmer/cm format (mandatory to use with --cm-db custom) (type: TEXT; default: ``)
  • --output-format: Output format for the combined results (type: CHOICE; default: tsv)
  • --motif-db: Database to use for RNA motif scanning - RolyPoly, jaspar_core, or a path to a folder containg a pwm/msa files (type: TEXT; default: RolyPoly)
  • -rm, --resolve-mode: How to deal with overlapping RNA element hits in the same sequence. - merge: all overlapping hits are merged into one range - one_per_range: one hit per range is reported - one_per_query: one hit per query sequence is reported - split: each overlapping element is split into a new row - drop_contained: hits that are contained within other hits are dropped - none: no resolution of overlapping hits is performed - simple: heuristic-based approach using drop_contained (type: CHOICE; default: simple)
  • -mo, --min-overlap-positions: Minimal number of overlapping positions between two intersecting ranges before they are considered as overlapping (used in some resolve_mode(s)). (type: INTEGER; default: 10)