# Pysam

Genomic file toolkit.

- Repository: https://github.com/LeonChaoX/qinyan-academic-skills (996 stars)
- Category: Writing
- License: MIT license
- Last updated: 2026-07-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add LeonChaoX/qinyan-academic-skills --skill pysam -g -a claude-code -y`
Codex: `npx skills add LeonChaoX/qinyan-academic-skills --skill pysam -g -a codex -y`
Cursor: `npx skills add LeonChaoX/qinyan-academic-skills --skill pysam -g -a cursor -y`
Gemini CLI: `npx skills add LeonChaoX/qinyan-academic-skills --skill pysam -g -a gemini-cli -y`

## 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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}")
samfile.close()
```

**Read variant file:**
```python
# Open VCF file and iterate variants
vcf = pysam.VariantFile("variants.vcf")
for variant in vcf:
    print(f"{variant.chrom}:{variant.pos} {variant.ref}>{variant.alts}")
vcf.close()
```

**Query reference sequence:**
```python
# Open FASTA and extract sequence
fasta = pysam.FastaFile("reference.fasta")
sequence = fasta.fetch("chr1", 1000, 2000)
print(sequence)
fasta.close()
```

## Core Capabilities

### 1. Alignment File Operations (SAM/BAM/CRAM)

Use the `AlignmentFile` class to work with aligned sequencing reads. This is appropriate for analyzing mapping results, calculating coverage, extracting reads, or quality control.

The rest: https://github.com/LeonChaoX/qinyan-academic-skills/blob/HEAD/skills/05-生物信息与基因组学/pysam/SKILL.md