bio

library1.8.3pypypi✓ verified 24d ago

The 'bio' library provides common bioinformatics algorithms and data structures implemented in Python. It is a lightweight alternative to larger bioinformatics packages, focusing on core functionalities like sequence manipulation, alignment, and motif analysis. The current version is 1.8.1, with a release cadence of a few updates per year, mainly for bug fixes and minor feature enhancements.

data ai-ml

pip install bio

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · BIO

bio

datapythonv1.8.3

Install

10.4s avg

Import

—

Disk

193MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.8.3 · 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 10.4s · import 0.000s · 187MB

193MB installed

● package 193MB

Code

Verified usage

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

Seq

✓ from bio.biorun import Seq

✗ from bio.biorun import Seq

This quickstart demonstrates basic sequence manipulation, including creating DNA sequences, obtaining reverse complements, transcribing to RNA, and translating to protein using the `bio.seq` module.

from bio import seq # Create a DNA sequence object dna_sequence = seq.Seq("ATGATCCAGGGC", seq.DNA) # Get the reverse complement reverse_complement = dna_sequence.rc() print(f"Original DNA: {dna_sequence}") print(f"Reverse complement: {reverse_complement}") # Get the RNA transcription rna_sequence = dna_sequence.transcribe() print(f"RNA: {rna_sequence}") # Translate to protein (starts from first codon) protein_sequence = rna_sequence.translate() print(f"Protein: {protein_sequence}")

Debug

Known issues

gotchaThe 'bio' library is distinct from 'Biopython'. While both handle bioinformatics, 'bio' is a smaller, more focused library by a different author. Do not confuse their APIs or expect interoperability without explicit conversion.

fix

Ensure you are importing from `bio` (e.g., `from bio import seq`) and refer to its specific documentation and API.

affects: All versions

gotchaSequence objects (e.g., `bio.seq.Seq`) are immutable. Methods like `.rc()`, `.transcribe()`, or `.translate()` return *new* `Seq` objects rather than modifying the original in-place. Always assign the result of these methods to a new variable.

fix

When performing operations on sequences, store the result: `new_seq = old_seq.operation()`. Do not expect `old_seq` to be modified.

affects: All versions

breakingThe 'bio' library requires Python 3.10 or newer. Attempting to install or run it on older Python versions (e.g., Python 3.9 or earlier) will result in installation failures or runtime errors.

fix

Ensure your development environment uses Python 3.10 or a later version. Upgrade Python if necessary or use a virtual environment with the correct Python version.

affects: 1.8.0+

Upgrade

Version history

1.8.3latest on PyPI · released May 11, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

26 hits · last 30 days

node

Amazon

OpenAI (training)

Resources

githubhttps://github.com/ialbert/bio#readme ↗

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

docshttps://github.com/ialbert/bio#readme ↗