Read write sequences

<!-- metadata: category: bioinformatics-sequence oversight: low version: 1.0.0 author: Pradyumna Jayaram tags: [bioinformatics-sequence, research] difficulty: intermediate -->

Read and Write Sequence Files

Hard rules

1. No fabricated citations. Every cited work must resolve to a verifiable
2. No claim without provenance. Every quantitative or factual claim
3. No silent failure. Every script invocation, API call, or tool use must declare its exit status and what to do on non-zero. A skill that silently swallows errors is a violation.

When to use

• Streaming reads from FASTA/FASTQ/GenBank/EMBL.
• Random access to a record by ID (huge files).
• Writing records back out, optionally after modification.
• Format conversion without touching record content.

When NOT to use

• BAM/SAM/CRAM/VCF → use pysam (see ors-bioinformatics-sequence-pysam-genomics).
• gzipped BAM/CRAM with random access → pysam.AlignmentFile.
• For >10 GB files, consider pyfastx (faster than Biopython for FASTA).

Prerequisites

• biopython>=1.83
• For indexed random access on BGZF FASTA, Biopython 1.83+ supports index() on .bgz.

Format strings (cheat sheet)

| Format | String | Notes | |--------|--------|-------|" | FASTA | "fasta" | Sequence only, single-line or wrapped | | FASTQ (Sanger / Illumina 1.8+) | "fastq" | Phred+33 | | FASTQ (Illumina 1.3-1.7) | "fastq-illumina" | Phred+64 | | FASTQ (Solexa) | "fastq-solexa" | Solexa+64 | | GenBank | "genbank" | Annotation + sequence | | EMBL | "embl" | EBI submission format | | SwissProt | "swiss" | UniProt curated | | UniProt XML | "uniprot-xml" | EBI download | | GFF3 | "gff3" | Genome features, not sequence records | | GTF | "gtf" | Gene transfer format | | ABI | "abi" | Sanger trace | | Phylip | "phylip" | Alignment | | Clustal | "clustal" | Alignment | | Stockholm | "stockholm" | Pfam/Rfam | | Tab-delimited | "tab" | ID, seq, optional qualifiers |

Code patterns

Stream parse

from Bio import SeqIO

for rec in SeqIO.parse("input.fasta", "fasta"):
    # rec.id, rec.description, rec.seq
    ...

List parse (small files only)

records = list(SeqIO.parse("small.fasta", "fasta"))

Indexed random access (huge FASTA)

from Bio import SeqIO

db = SeqIO.index("large.fasta", "fasta")
seq = db["target_id"].seq
db.close()

For persistent index (no rebuild on next open):

db = SeqIO.index_db("large.idx", "large.fasta", "fasta")

Indexed BGZF random access

db = SeqIO.index("indexable.fasta.bgz", "fasta")

Write records (single file, multiple records)

from Bio import SeqIO

SeqIO.write(records, "out.fasta", "fasta")

The return value is the number of records written.

Write one record at a time

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq

with open("out.fasta", "w") as fh:
    rec = SeqRecord(Seq("ACGT"), id="seq1", description="example")
    SeqIO.write(rec, fh, "fasta")

Append records across formats (streaming)

from Bio import SeqIO

def stream_to_fasta(in_path, in_fmt, out_path):
    with open(out_path, "w") as out:
        for rec in SeqIO.parse(in_path, in_fmt):
            # modify rec if needed
            SeqIO.write(rec, out, "fasta")

Convert without touching records

from Bio import SeqIO
n = SeqIO.convert("in.gb", "genbank", "out.fasta", "fasta")
print(f"Converted {n} records")

Handle FASTA with wrapped multi-line sequences

Biopython auto-handles wrapped FASTA in parse(); record.seq is always the full sequence.

Parse GenBank with features

from Bio import SeqIO

for rec in SeqIO.parse("annotation.gb", "genbank"):
    for feat in rec.features:
        if feat.type == "CDS":
            gene = feat.qualifiers.get("gene", ["?"])[0]
            print(gene, feat.location)

Parse BLAST tab output

from Bio import SeqIO
for qresult in SeqIO.parse("blast.tab", "blast-tab"):
    for hsp in qresult:
        ...

blast-tab parses the tabular -outfmt 6.

Truncate IDs to first whitespace

def short_id(rec):
    rec.id = rec.id.split()[0]
    rec.description = ""
    return rec

Common pitfalls

• Mixing parse() with index() and forgetting to close the index. Index files hold file handles; use a context manager or explicit close().
• Indexed access on a .fasta.gz (plain gzip) fails. Convert to BGZF first.
• Write format mismatch. If you parsed with "fastq-illumina" and wrote with "fastq", Biopython re-encodes qualities. Usually fine, but worth being explicit.
• Mismatched record count from SeqIO.convert. Returns 0 silently if source format is wrong. assert n > 0.
• Header pollution. FASTA identifiers stop at first whitespace; multi-word descriptions go into description. If you write a record with both id="seq1 chr1" and a description, downstream tools will see seq1 as the ID.

Validation

• n_records_in == n_records_out for round-trips.
• For indexed access: db["known_id"].seq == expected_seq.
• For GenBank round-trips: len(features_in) == len(features_out), modulo per-format feature filtering.

Open alternatives

Need	Tool
Faster FASTA parsing	pyfastx
Format conversion at scale	seqkit convert, bioawk
Random access to huge FASTA	samtools faidx + bgzip
GFF/GTF parsing	gffutils, pyranges

References

• Biopython SeqIO: https://biopython.org/docs/latest/api/Bio.SeqIO.html
• Format list: https://biopython.org/wiki/SeqIO#File_Formats
• Companion: ors-bioinformatics-sequence-format-conversion, ors-bioinformatics-sequence-compressed-sequence-files.

Changelog

• 1.0.0 (2026-06-10): Initial adaptation by Pradyumna Jayaram from bio-read-sequences and bio-write-sequences (bioSkills-main/sequence-io/).

Cross-references

Other skills in this category:

• batch-processing
• bowtie2-alignment
• bwa-alignment
• bwa-mem2-alignment
• codon-usage
• compressed-sequence-files
• fastq-quality-scores
• filter-sequences
• format-conversion
• hisat2-alignment
• motif-search
• paired-end-fastq
• pysam-genomics
• reverse-complement
• sam-bam-basics
• samtools-bam-processing
• seq-objects
• sequence-properties
• sequence-slicing
• sequence-statistics
• star-alignment
• transcription-translation