Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add fmschulz/omics-skills --skill bio-fasta-database-curatorgit clone --depth 1 https://github.com/fmschulz/omics-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/fmschulz/omics-skills/bio-fasta-database-curator)<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-fasta-database-curator"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-fasta-database-curator/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-fasta-database-curator"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-fasta-database-curator.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00050 | $0.02108 |
| Opus 5.5 | $0.00020 | $0.00843 |
| Sonnet 5.5 | $0.00010 | $0.00422 |
| Haiku 4.5 | $0.00005 | $0.00211 |
Grade A, and why
bio-fasta-database-curator scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 23d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 215 lines — stays where its author put it; the contents beside it link to each section on GitHub.
FASTA Database Curator
Curate FASTA/FAA reference databases: standardize headers, merge files, remove duplicates, and validate the result for BLAST, DIAMOND, MMseqs2, or HMMER. Every transformation leaves a header mapping and a deduplication report.
Supplementary version-grounded tool notes: tools.md.
Header Format Standards
Recommended Format
Use pipe-separated fields with a consistent source prefix:
>PREFIX|ACCESSION|DESCRIPTION
SEQUENCE...
Examples:
>VP|Mavirus_MCP|Major_capsid_protein_[Virophage]
>PLV|NC_021333_1|Polinton-like_virus_hypothetical_protein
>NCLDV|YP_009173877.1|DNA_polymerase_[Marseilleviridae]
What the bundled script does
scripts/curate_fasta.py keeps the whole raw header, replaces each whitespace run and each character outside A-Za-z0-9_.|:- with _, collapses repeated _, and prepends PREFIX| when --prefix is set:
>seq 1 alpha protein -> >REF|seq_1_alpha_protein
>NC_021333.1 hypothetical -> >REF|NC_021333.1_hypothetical
Split accession and description into separate pipe fields with a custom rule, and keep the mapping table for it as well.
BLAST makeblastdb -parse_seqids reads | as NCBI seq-id syntax and fails on custom prefixes such as VP|... ("Could not construct seq-id"). Build pipe-delimited databases without -parse_seqids. DIAMOND, MMseqs2, and HMMER keep the full first word of the header.
Quick Reference
| Task | Action |
|---|---|
| Inspect database | Count records, sample headers, check whitespace and length distribution before changing anything. |
| Standardize headers | Define deterministic transformation rules and preserve original-to-new ID mapping. |
| Merge or deduplicate | Decide whether duplicates are removed by ID, sequence, or both, then report what changed. |
| Validate output | Re-count records, verify FASTA syntax, and write database statistics. |
| Run the bundled curator | uv run --script skills/bio-fasta-database-curator/scripts/curate_fasta.py input.fasta --output curated.fasta --prefix REF --deduplicate both |
| Build search databases | Commands for makeblastdb, diamond makedb, mmseqs createdb, and hmmpress in tools.md. |
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 23d ago Changed · -46 lines · -2 tokens per session c981f29daaca
- 1mo ago Changed 282dd87ebaae
- 1mo ago First seen · 261 lines · 52 tokens per session scan A 47bcbc6a6578
bio-fasta-database-curator is a skill published in the GitHub repository fmschulz/omics-skills (11 stars, last pushed 23d ago), licensed MIT. It adds 50 tokens to every session and 2,108 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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