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Skillsncbi-blast-skill

ncbi-blast-skill

Coding & development

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Updated 10-16 03:05

About this skill

Operating rules

  • Use scripts/ncbi_blast.py for all concrete BLAST work.
  • Honor NCBI limits: >=10s between requests and >=60s between polls for the same RID.
  • Always surface the RID in the response so the job can be resumed or refetched later.
  • If the conversation is long or multiple tool calls have occurred, refetch from the RID instead of trusting older context.
  • If a prior turn saved raw output to disk, do not read it back into context unless the user asks for a specific follow-up.

Execution behavior

  • Return compact BLAST summaries first.
  • Do not paste full JSON2 or long Text alignments into chat by default.
  • Default to max_hits=5 and max_queries=5.
  • If the user asks for raw output, write it to a file and report the path.
  • Only provide Python code when the user explicitly asks for code or execution is unavailable.
  • For normal user-facing answers, summarize the script JSON in markdown; if the user explicitly asks for machine-readable output, return the JSON verbatim.

Input

  • The script reads one JSON object from stdin.
  • action must be one of submit, status, fetch, or run.
  • submit and run require program, database, query_fasta, and email (or NCBI_EMAIL).
  • status and fetch require rid.
  • program must be one of blastn, blastp, blastx, tblastn, or tblastx.
  • result_format defaults to json2 for run and fetch.
  • tool defaults to NCBI_TOOL, then ncbi-blast-skill.
  • max_hits defaults to 5; max_queries defaults to 5.
  • hitlist_size defaults to 50; descriptions and alignments default to 5.
  • wait_timeout_sec defaults to 900.
  • save_raw defaults to false.
  • If save_raw=true and raw_output_path is omitted, the script writes to /tmp/ncbi-blast-<rid>.<json|txt>.
  • query_fasta may contain multi-FASTA input; compact summaries still cap per-query output with max_hits and max_queries.

Output

  • Common success fields: ok, source, action, warnings.
  • submit returns rid, rtoe_seconds, and status="SUBMITTED".
  • status returns rid, normalized status, and has_hits.
  • run and fetch with result_format=json2 return rid, status, has_hits, result_format, query_count_returned, query_count_available, query_summaries_truncated, query_summaries, and raw_output_path.
  • Each query_summary contains query_title, hit_count_returned, hit_count_available, truncated, and top_hits.
  • Each top_hit contains rank, accession, title, evalue, and bit_score.
  • fetch with result_format=text returns text_head capped at 800 characters unless save_raw=true; when save_raw=true, it returns only the artifact path.
  • Failures return ok=false, error.code, error.message, and warnings.

Execution

  • Run python scripts/ncbi_blast.py.
  • If requests is missing, install it once before first use with python -m pip install requests.
echo '{"action":"run","program":"blastp","database":"swissprot","query_fasta":">q1\nMTEYK...","email":"you@example.com"}' | python scripts/ncbi_blast.py

References

  • Load references/blast-common-url-api.txt only for parameter details or uncommon BLAST options.
  • Do not load references/intent-notes.txt during normal skill execution; it is not runtime guidance.