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

If the request is about installation or setup, read rpsblast-reference.md.
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.
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
If rpsbproc will be used, force rpsblast/rpstblastn output to ASN.1 archive format with -outfmt 11 and save it as <prefix>.asn.
Run rpsbproc on the ASN.1 file to produce <prefix>.out.
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
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