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Rdrp Motif Search

Summary

Search for RdRp motifs (A, B, C, D) in nucleotide or amino acid sequences.

Description

This command searches input sequences for RNA-dependent RNA polymerase (RdRp) motif patterns using pre-built profile databases from the RVMT project.

The output is a table with one row per input sequence, showing motif locations, scores, and conformations found.

Usage

rolypoly rdrp-motif-search [OPTIONS]

Options

  • -i, --input: Input FASTA file with nucleotide or amino acid sequences (type: TEXT; required; default: Sentinel.UNSET)
  • -o, --output: Output directory path (type: TEXT; default: ./rdrp_motif_search_output)
  • -e, --evalue: E-value threshold for motif searches (type: FLOAT; default: 0.01)
  • --min-score: Minimum score threshold for motif matches (type: FLOAT)
  • --max-distance: Maximum distance between motifs in amino acids (type: INTEGER; default: 250)
  • --search-tool: No description provided. (type: CHOICE; default: hmmsearch)
  • --aa-method: Method for amino acid translation from nucleotides (type: CHOICE; default: six_frame)
  • --min-orf-length: Minimum ORF length for gene prediction (type: INTEGER; default: 30)
  • --motif-filter: Filter results by specific motif type (type: CHOICE)
  • --no-include-alignment: Disable including aligned region sequences in output (alignment included by default) (type: BOOLEAN; default: False)
  • --data-dir: Path to rolypoly data directory (if not in default location) (type: TEXT)
  • --output-format: Output file format (tsv or parquet) (type: CHOICE; default: tsv)
  • --output-structure: Output structure: nested (motif_details as JSON) or flat (separate columns per motif) (type: CHOICE; default: nested)
  • -ow, --overwrite: Overwrite output directory if it exists (type: BOOLEAN; default: False)
  • -cf, --config-file: JSON config file with parameters (overrides command line) (type: TEXT)
  • -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)
  • -td, -tmp, --temp-dir: Temporary working directory. (type: DIRECTORY)
  • -g, --log-file: Path to the log file. (type: FILE; default: rolypoly.log)

Additional Notes

EXAMPLES:

  # Basic search with default flat TSV output and alignment
  rolypoly rdrp-motif-search -i sequences.fasta -o results_dir

  # Nested structure for programmatic analysis
  rolypoly rdrp-motif-search -i sequences.fasta -o results_dir --output-structure nested

  # Parquet output with structured data for analysis
  rolypoly rdrp-motif-search -i sequences.fasta -o results_dir --output-format parquet

  # Disable alignment to reduce output size
  rolypoly rdrp-motif-search -i sequences.fasta -o results_dir --no-include-alignment

  # High sensitivity search with custom parameters
  rolypoly rdrp-motif-search -i sequences.fasta -o results_dir -e 0.1 --max-distance 300

OUTPUT FORMATS:

  flat + tsv: separate columns (motif_a_start, motif_b_start, etc.) - DEFAULT
  nested + tsv: motif_details column as JSON string
  flat + parquet: separate columns with native data types
  nested + parquet: motif_details as structured data types