sequence_files

Pysam provides the FastaFile class for indexed, random access to FASTA reference sequences. FASTA files must be indexed with samtools faidx before use.

Skills
Scientific
0

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.

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Install (Claude Code)

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

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

Content

# Working with Sequence Files (FASTA/FASTQ)

## FASTA Files

### Overview

Pysam provides the `FastaFile` class for indexed, random access to FASTA reference sequences. FASTA files must be indexed with `samtools faidx` before use.

### Opening FASTA Files

```python
import pysam

# Open indexed FASTA file
fasta = pysam.FastaFile("reference.fasta")

# Automatically looks for reference.fasta.fai index
```

### Creating FASTA Index

```python
# Create index using pysam
pysam.faidx("reference.fasta")

# Or using samtools command
pysam.samtools.faidx("reference.fasta")
```

This creates a `.fai` in

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