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)
• -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 (PSSM search). Not fully supported yet. (type: CHOICE; default: lightmotif)
• --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. (type: CHOICE; default: simple)

  • 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

• -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)

• -t, --threads: Number of worker threads. (type: INTEGER RANGE; default: 1)
• -M, --memory: Memory limit, for example 8g. (type: MEMORY; default: 8g)
• -g, --log-file: Path to the log file. (type: FILE; default: rolypoly.log)