dnaio

library1.2.4pypypi✓ verified 86d ago

A Python library for reading and writing FASTA and FASTQ files efficiently. Current version 1.2.4, released periodically with active development. It provides a simple iterator-based API and supports compression.

data serialization

pip install dnaio

github ↗package ↗homepage ↗changelog ↗

INSTALL

IMPORT

SIG · DNAIO

dnaio

datapythonv1.2.4

Install

2.0s avg

Import

116ms

Disk

19MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.2.4 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 2.0s · import 0.116s · 22MB

19MB installed

● package 19MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

open

✓ import dnaio

Main entry point; use dnaio.open() to read/write sequence files.

SequenceRecord

✓ from dnaio import SequenceRecord

Data class for sequence records.

Basic usage: read and write FASTA/FASTQ using dnaio.open(). Records have .name, .sequence, .qual attributes.

import dnaio with dnaio.open('example.fasta') as f: for record in f: print(record.name, record.sequence) # Writing with dnaio.open('output.fasta', mode='w') as f: f.write(dnaio.SequenceRecord('seq1', 'ACGT'))

Debug

Known issues

gotchadnaio.open() returns an iterator, not a list. If you need random access or indexing, load records into a list first.

fix

records = list(dnaio.open('file.fastq'))

affects: all

deprecatedThe old dnaio.read() and dnaio.write() functions are deprecated since version 1.0. Use dnaio.open() instead.

fix

Replace dnaio.read('file') with dnaio.open('file') and dnaio.write('file', records) with dnaio.open('file', mode='w') as f: for r in records: f.write(r)

affects: >=1.0

gotchaFASTQ quality scores are automatically converted to Phred+33; if your file uses Phred+64, you must specify quality_scale=64.

fix

with dnaio.open('file.fastq', quality_scale=64) as f: ...

affects: all

Errors

Common errors & fixes

AttributeError: module 'dnaio' has no attribute 'read'

The legacy dnaio.read() and dnaio.write() functions were removed in version 1.0.0.

fix

Use dnaio.open() instead: with dnaio.open('file.fasta') as f: for record in f: ...

TypeError: '_io.TextIOWrapper' object is not iterable

Calling dnaio.open() on a file object without specifying format or mode correctly.

fix

Pass the filename as a string, not a file object. Ensure mode is 'r' (default) for reading.

Upgrade

Version history

1.2.4latest on PyPI · released Oct 12, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

15 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/marcelm/dnaio ↗

packagehttps://pypi.org/project/dnaio/ ↗

homepagehttps://dnaio.readthedocs.io/ ↗

changeloghttps://dnaio.readthedocs.io/en/latest/changes.html ↗