Sequence I/O

Read, write, and manipulate biological sequence files (FASTA, GenBank, FASTQ).

When to Use This Skill

This skill should be used when:

• Reading or writing sequence files (FASTA, GenBank, FASTQ)

• Converting between sequence file formats

• Manipulating sequences (complement, reverse complement, translate)

• Extracting sequences from large indexed FASTA files (faidx)

• Calculating sequence statistics (GC content, molecular weight, Tm)

When NOT to Use This Skill

• NGS alignment files (SAM/BAM/VCF) → Use pysam

• BLAST searches → Use gget (quick) or blat-integration (large-scale)

• Multiple sequence alignment → Use msa-advanced

• Phylogenetic analysis → Use etetoolkit

• NCBI database queries → Use pubmed-database or gene-database

Tool Selection Guide

Task Tool Reference

Parse FASTA/GenBank/FASTQ Bio.SeqIO

biopython_seqio.md

Convert file formats Bio.SeqIO.convert()

biopython_seqio.md

Sequence operations Bio.Seq

biopython_seqio.md

Large FASTA random access pysam.FastaFile

• faidx faidx.md

GC%, Tm, molecular weight Bio.SeqUtils

utilities.md

Quick Start

Installation

uv pip install biopython pysam

Read FASTA

from Bio import SeqIO

for record in SeqIO.parse("sequences.fasta", "fasta"): print(f"{record.id}: {len(record.seq)} bp")

Convert GenBank to FASTA

from Bio import SeqIO

SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")

Random Access with faidx

import pysam

Create index (once)

pysam.faidx("reference.fasta")

Random access

fasta = pysam.FastaFile("reference.fasta") seq = fasta.fetch("chr1", 1000, 2000) # 0-based coordinates fasta.close()

Sequence Operations

from Bio.Seq import Seq

seq = Seq("ATGCGATCGATCG") print(seq.complement()) print(seq.reverse_complement()) print(seq.translate())

Reference Documentation

Consult the appropriate reference file for detailed documentation:

references/biopython_seqio.md

• Bio.Seq object and sequence operations

• Bio.SeqIO for file parsing and writing

• SeqRecord object and annotations

• Supported file formats

• Format conversion patterns

references/faidx.md

• Creating FASTA index with pysam.faidx()

• pysam.FastaFile for random access

• Coordinate systems (0-based vs 1-based)

• Performance considerations for large files

• Common patterns (variant context, gene extraction)

references/utilities.md

• GC content calculation (gc_fraction )

• Molecular weight (molecular_weight )

• Melting temperature (MeltingTemp )

• Codon usage analysis

• Restriction enzyme sites

references/formats.md

• FASTA format specification

• GenBank format specification

• FASTQ format and quality scores

• Format detection and validation

Coordinate Systems

Biopython: Uses Python-style 0-based, half-open intervals for slicing.

pysam.FastaFile.fetch():

• Numeric arguments: 0-based (fetch("chr1", 999, 2000) = positions 999-1999)

• Region strings: 1-based (fetch("chr1:1000-2000") = positions 1000-2000)

Common Pitfalls

• Coordinate confusion: Remember which tool uses 0-based vs 1-based

• Missing faidx index: Random access requires .fai file

• Format mismatch: Verify file format matches the format string in SeqIO.parse()

• Iterator exhaustion: SeqIO.parse() returns an iterator; convert to list if multiple passes needed

• Large files: Use iterators, not list() , for memory efficiency