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rpsblast-assistant

Use natural language to prepare, run, and interpret standalone rpsblast, rpstblastn, and rpsbproc workflows against NCBI CDD assets.

personAuthor: TashanworldhubOpenAPI
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Skill: rpsblast-assistant

Use When

  • A user wants to install or prepare standalone rpsblast, rpstblastn, or rpsbproc.
  • A user wants the agent to download and unpack the CDD databases or rpsbproc annotation files.
  • A user wants to run CDD/RPS-BLAST locally from natural language instead of hand-writing commands.
  • A user needs help understanding which files are required, how to structure the project folder, or what output formats are produced.
  • A user wants the post-processed tabular annotations from rpsbproc, not just raw BLAST output.

Inputs

  • Required:
    • query FASTA path, sequence text, or a request to prepare the environment only
  • Optional:
    • query type: protein or nucleotide
    • database prefix, usually db/Cdd
    • output prefix
    • E-value threshold
    • whether to run rpsbproc
    • location of local binaries or downloaded archives

Workflow

  1. If the request is about installation or setup, read rpsblast-reference.md.
  2. Prefer the canonical local pipeline:
    • scripts/run.sh sources to print acquisition URLs.
    • scripts/run.sh download --db-dir db --data-dir data to fetch and unpack the CDD database and annotation files.
    • scripts/run.sh check --db-prefix <prefix> --data-dir <dir> to verify a local setup.
    • scripts/run.sh run --query <fasta> --db-prefix <prefix> --out-prefix <prefix> to execute the pipeline.
  3. Translate natural language into explicit parameters:
    • default to protein unless the user clearly asks for nucleotide queries
    • use rpsblast for proteins and rpstblastn for nucleotide input
    • default E-value to 0.01 for the paper's standard local workflow unless the user requests another threshold
    • default to post-processing with rpsbproc
    • for database download requests, default to --db-set minimal unless the user asks for the full external-source collection
  4. If rpsbproc will be used, force rpsblast/rpstblastn output to ASN.1 archive format with -outfmt 11 and save it as <prefix>.asn.
  5. Run rpsbproc on the ASN.1 file to produce <prefix>.out.
  6. Report:
    • exact command(s) run
    • generated file paths
    • whether the final result is raw ASN.1 archive output or post-processed tab-delimited annotations
    • for rpsbproc output, mention that the file begins with comment/template lines starting with # and then a structured data section
    • a brief interpretation of the result file
  7. If the environment is incomplete, stop and tell the user exactly which binary, database, or data file is missing.

Output Contract

  • Setup guidance that names the source URLs for:
    • BLAST+ executables containing rpsblast/rpstblastn
    • rpsbproc
    • CDD little_endian databases
    • CDD annotation/data files
  • A runnable command line or a completed execution using scripts/run.sh
  • For download flows, a populated db/ and optionally data/ directory, plus the original archives under a download cache directory
  • Generated files, typically:
    • <prefix>.asn: ASN.1 archive output from rpsblast/rpstblastn
    • <prefix>.out: tab-delimited flat file from rpsbproc, with a comment/template header and a data section delimited by DATA and ENDDATA
  • A short natural-language summary of what the output means

Limits

  • This skill does not bundle NCBI binaries or CDD databases.
  • The download helper fetches official public files but still depends on local network access and the NCBI FTP/HTTPS endpoints being reachable.
  • rpsbproc requires raw rpsblast/rpstblastn output in ASN.1 archive format; plain text or tabular BLAST output is not sufficient for post-processing.
  • rpsbproc output is not just a plain spreadsheet dump; parsers should ignore leading # comment/template lines and read the structured data section.
  • The paper notes that standalone rpsblast is time-consuming for large batches; use expectations accordingly.
  • Common failure cases:
    • downloading only databases but forgetting the annotation files needed by rpsbproc
    • using the wrong executable for query type
    • pointing -db at the directory instead of the database prefix
    • forgetting the CDD annotation files required by rpsbproc
    • emitting the wrong -outfmt when rpsbproc is needed
    • assuming the final .out file is BLAST pairwise text rather than tab-delimited annotations