alignment_files

Pysam provides the AlignmentFile class for reading and writing SAM/BAM/CRAM formatted files containing aligned sequence data. BAM/CRAM files support compression and random access through indexing.

Skills
Scientific
3

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/alignment-files && curl -fsSL https://doutorai.pt/data/lib/skills__alignment-files.md -o .claude/skills/alignment-files/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# Working with Alignment Files (SAM/BAM/CRAM)

## Overview

Pysam provides the `AlignmentFile` class for reading and writing SAM/BAM/CRAM formatted files containing aligned sequence data. BAM/CRAM files support compression and random access through indexing.

## Opening Alignment Files

Specify format via mode qualifier:
- `"rb"` - Read BAM (binary)
- `"r"` - Read SAM (text)
- `"rc"` - Read CRAM (compressed)
- `"wb"` - Write BAM
- `"w"` - Write SAM
- `"wc"` - Write CRAM

```python
import pysam

# Reading
samfile = pysam.AlignmentFile("example.bam", "rb")

# Writing (requires template or header

- 🔒 Full content on the Pro plan (€7.99/month) -

Need help with Claude Code?

Ask Dr AI - it explains things simply.

Need a tailor-made solution?

Not sure where to start with AI in your business? Get a free assessment and a tailored plan - no commitment.

Save hours every week with AI, no hassle

Doutor AI gives you 1,859 ready-to-copy AI prompts, by industry and in plain English - plus a complete technical library for those who want to go further.

See plans