Skill · em Dados, IA e pesquisa

pysam

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/pysam
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
1 download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

5 arquivos · 53,6 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/pysam/.

d=".claude/skills/pysam"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pysam"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/alignment_files.md" "$u/references/alignment_files.md" \
  -o "$d/references/common_workflows.md" "$u/references/common_workflows.md" \
  -o "$d/references/sequence_files.md" "$u/references/sequence_files.md" \
  -o "$d/references/variant_files.md" "$u/references/variant_files.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/pysam/.

d="$HOME/.claude/skills/pysam"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pysam"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/alignment_files.md" "$u/references/alignment_files.md" \
  -o "$d/references/common_workflows.md" "$u/references/common_workflows.md" \
  -o "$d/references/sequence_files.md" "$u/references/sequence_files.md" \
  -o "$d/references/variant_files.md" "$u/references/variant_files.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/pysam/.

d=".agents/skills/pysam"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pysam"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/alignment_files.md" "$u/references/alignment_files.md" \
  -o "$d/references/common_workflows.md" "$u/references/common_workflows.md" \
  -o "$d/references/sequence_files.md" "$u/references/sequence_files.md" \
  -o "$d/references/variant_files.md" "$u/references/variant_files.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/pysam/.

d="$HOME/.agents/skills/pysam"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pysam"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/alignment_files.md" "$u/references/alignment_files.md" \
  -o "$d/references/common_workflows.md" "$u/references/common_workflows.md" \
  -o "$d/references/sequence_files.md" "$u/references/sequence_files.md" \
  -o "$d/references/variant_files.md" "$u/references/variant_files.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/pysam/.

d=".agents/skills/pysam"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pysam"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/alignment_files.md" "$u/references/alignment_files.md" \
  -o "$d/references/common_workflows.md" "$u/references/common_workflows.md" \
  -o "$d/references/sequence_files.md" "$u/references/sequence_files.md" \
  -o "$d/references/variant_files.md" "$u/references/variant_files.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/pysam/.

d="$HOME/.gemini/antigravity-cli/skills/pysam"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pysam"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/alignment_files.md" "$u/references/alignment_files.md" \
  -o "$d/references/common_workflows.md" "$u/references/common_workflows.md" \
  -o "$d/references/sequence_files.md" "$u/references/sequence_files.md" \
  -o "$d/references/variant_files.md" "$u/references/variant_files.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.pysam

Prévia do SKILL.md

---
name: pysam
description: "Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines."
---

# Pysam

## Overview

Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.

## When to Use This Skill

This skill should be used when:
- Working with sequencing alignment files (BAM/CRAM)
- Analyzing genetic variants (VCF/BCF)
- Extracting reference sequences or gene regions
- Processing raw sequencing data (FASTQ)
- Calculating coverage or read depth
- Implementing bioinformatics analysis pipelines
- Quality control of sequencing data
- Variant calling and annotation workflows

## Quick Start

### Installation
```bash
uv pip install pysam
```

### Basic Examples

**Read alignment file:**
```python
import pysam

# Open BAM file and fetch reads in region
samfile = pysam.AlignmentFile("example.bam", "rb")
for read in samfile.fetch("chr1", 1000, 2000):
    print(f"{read.query_name}: {read.reference_start}")
…

Ver todo o marketplace