pysam

pysam is a skill for Claude Code, Codex from wu-yc/LabClaw. It costs 47 tokens per session (2,469 once invoked), scanned A, original, no licence file.

A Python toolkit for working with common genomics files, including DNA sequences, genetic variants, and sequencing read alignments. It is designed for next-generation sequencing data pipelines.

In plain words
What is it for?
Read and write SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ files; extract regions; and calculate coverage.
Why use it?
It avoids writing separate file parsers and data-handling code for each genomics format. It also helps locate genomic regions and measure sequencing coverage.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Read and write SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ files…

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/wu-yc/labclaw/pysam
Install

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.

Any agent
npx skills add wu-yc/LabClaw --skill pysam
Clone the repo
git clone --depth 1 https://github.com/wu-yc/LabClaw

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for pysam

README.md
[![agentmods](https://agentmods.dev/badge/skills/wu-yc/labclaw/pysam.svg)](https://agentmods.dev/skills/wu-yc/labclaw/pysam)
Your own site
<a href="https://agentmods.dev/skills/wu-yc/labclaw/pysam"><img src="https://agentmods.dev/badge/skills/wu-yc/labclaw/pysam.svg" alt="Measured on agentmods" height="20"></a>
Per session 47 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,469 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00047 $0.02469
Opus 5 $0.00023 $0.01234
Sonnet 5 $0.00009 $0.00494
Haiku 4.5 $0.00005 $0.00247

Measured 7d ago against content hash 9f06b4b3df4a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-06, from the pricing page.

Security

Grade A, and why

pysam 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 7d 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.

Without an index, use `fetch(until_eof=True)` for sequential reading.
skills/bio/pysam/SKILL.md · 265 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Changes

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.

  1. 7d ago First seen · 265 lines · 47 tokens per session scan A 9f06b4b3df4a

Subscribe to this mod's changes

pysam is a skill published in the GitHub repository wu-yc/LabClaw (1,049 stars, last pushed 5mo ago), with no licence file. It adds 47 tokens to every session and 2,469 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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