bio

What it is and what it does

bio is a command-line toolkit designed to reduce the friction of routine bioinformatics tasks. It wraps common operations—fetching sequences from GenBank, converting between FASTA/GFF/VCF formats, aligning sequences, and querying taxonomic lineages—into short, composable commands that can be chained together using Unix pipes. The package is built on biopython, mygene, gprofiler-official, and other established bioinformatics libraries, and is oriented toward stream processing so that output from one command naturally feeds into the next.

The project is in active beta and targets students, educators, and researchers working with similar genomes (bacterial or viral strains) or investigating specific genomic regions. It aims to replace multi-step workflows and arcane command sequences with explicit, readable commands. The toolkit is maintained actively and supports Python 3.10 through 3.12.

Use it for:

• Fetch viral or bacterial genome sequences by accession number and convert them to FASTA or GFF format for downstream analysis.
• Extract and align coding sequences for a specific gene across multiple genomes, then generate variant calls in VCF format.
• Query taxonomic lineages and descendants for a given taxon ID to understand evolutionary relationships.
• Teach bioinformatics concepts in a classroom setting using readable, composable commands rather than complex scripting.
• Investigate precise details of a genomic region by combining fetch, format conversion, and alignment in a single pipeline.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

A command-line toolkit that simplifies common bioinformatics tasks like fetching sequences, converting formats, aligning genomes, and querying taxonomic data through composable commands.

Yes, if you work with genomic data and want to reduce command-line friction. The package is actively maintained, has no known vulnerabilities, uses a permissive MIT license, and depends on stable bioinformatics libraries. It is explicitly designed for learning and exploration, so it suits educational and investigative use well. Consider whether its command set covers your specific workflows before committing to it as a primary tool.

Install

bio on PyPI

pip install bio

uv add bio

poetry add bio

Installing bio

Before you install

Low friction installation as a pure Python wheel. Active maintenance with recent releases; last commit 2026-05-11. Depends on established bioinformatics libraries (biopython, mygene, gprofiler-official) and common utilities (pandas, requests, tqdm, pooch).

License in practice

MIT license permits commercial and private use with minimal restrictions, making it suitable for both educational and production bioinformatics workflows.

Quickstart

pip install bio

bio fetch NC_045512 > genome.gb
bio fasta genome.gb --end 10

Requires Python 3.10 or later (supports 3.10, 3.11, 3.12); works on Linux, Mac, and Windows with Linux Subsystem.

Verify before relying

• Whether all runtime dependencies (biopython, gprofiler-official, mygene) install reliably across all supported Python versions without system-level prerequisites.
• Performance characteristics when processing large genomic datasets or deeply nested taxonomic queries.
• Stability of external data sources (GenBank, taxonomic databases) that bio queries.

Package facts

Evidence: bio-1.8.3-py3-none-any.whl

Tags

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