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 PKU-YuanGroup/OpenAI4S --skill bio-alignment-files-reference-operationsgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-alignment-files-reference-operations)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-reference-operations"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-reference-operations/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/pku-yuangroup/openai4s/bio-alignment-files-reference-operations"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-reference-operations.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00032 | $0.03395 |
| Opus 5 | $0.00016 | $0.01698 |
| Sonnet 5 | $0.00006 | $0.00679 |
| Haiku 4.5 | $0.00003 | $0.00340 |
Grade A, and why
bio-reference-operations scanned grade A with 1 finding 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 12d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
seq = ref.fetch(chrom) This is a copy
94% identical to bio-reference-operations — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 385 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: GATK 4.5+, bcftools 1.19+, pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Reference Operations
Generate consensus sequences and manage reference files using samtools.
"Prepare a reference genome" -> Index the FASTA and create a sequence dictionary for downstream tools.
- CLI:
samtools faidx ref.fa+samtools dict ref.fa -o ref.dict - Python:
pysam.FastaFile('ref.fa')(auto-uses .fai index)
"Build a consensus from BAM" -> Derive the most-supported base at each position from aligned reads.
- CLI:
samtools consensus input.bam -o consensus.fa - Python: iterate pileup columns and take majority base (pysam)
samtools faidx - Index Reference FASTA
Create index for random access to reference sequences.
Create Index
samtools faidx reference.fa
# Creates reference.fa.fai
Fetch Region from Reference
samtools faidx reference.fa chr1:1000-2000
Fetch Multiple Regions
samtools faidx reference.fa chr1:1000-2000 chr2:3000-4000
Fetch Entire Chromosome
samtools faidx reference.fa chr1
Output to File
samtools faidx reference.fa chr1:1000-2000 > region.fa
Reverse Complement
samtools faidx -i reference.fa chr1:1000-2000
FAI File Format
chr1 248956422 6 60 61
chr2 242193529 253105708 60 61
Columns: name, length, offset, line bases, line width
samtools dict - Create Sequence Dictionary
Create SAM header dictionary for reference (used by GATK, Picard).
Create Dictionary
samtools dict reference.fa -o reference.dict
What ships with it
2 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.
- 12d ago First seen · 385 lines · 32 tokens per session scan A 485407fda65e
bio-reference-operations is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 32 tokens to every session and 3,395 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 94% identical to bio-reference-operations, differing in 12 lines, and is treated as a copy.
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