bioutils

library0.6.1pypypi✓ verified 84d ago

A library of miscellaneous simple bioinformatics utilities and lookup tables, including codon translation, sequence manipulation, and assembly mapping. Current version 0.6.1, requires Python >=3.10, maintained by biocommons.

data

pip install bioutils

github ↗package ↗

INSTALL

IMPORT

SIG · BIOUTILS

bioutils

datapythonv0.6.1

Install

2.2s avg

Import

—

Disk

20MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.6.1 · 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

installs and imports cleanly · install 0.0s · import 0.000s · 22.1MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 2.2s · import 0.000s · 23MB

20MB installed

● package 20MB

Code

Verified usage

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

PackageNotFoundError

✓ from bioutils import PackageNotFoundError

✗ from bioutils import codons

version

✓ from bioutils import version

✗ from bioutils import codons

Demonstrates basic codon translation and sequence manipulation.

from bioutils import codons, sequences # Translate a DNA sequence to protein dna = "ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG" protein = codons.translate(dna) print(protein) # Get reverse complement rev_comp = sequences.reverse_complement(dna) print(rev_comp)

bioutils --version

Debug

Known issues

breakingVersion 0.6.0 dropped support for Python <3.10 and migrated configuration from setup.cfg to pyproject.toml. If you are on an older Python version, stay on 0.5.x.

fix

Upgrade to Python >=3.10 or pin bioutils to <0.6.0.

affects: >=0.6.0

gotchaFunctions like codons.translate() and sequences.reverse_complement() expect plain string input, not Bio.Seq objects. Passing a Seq object will cause a TypeError.

fix

Convert Seq objects to string using str(seq) before passing to bioutils functions.

affects: all

Upgrade

Version history

0.6.1latest on PyPI · released Nov 4, 2024

Audit

Dependencies

biopythonrequiredRequired for sequence I/O and biological sequence objects

requestsrequiredUsed for online assembly lookups and NCBI API calls

Agent activity

18 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/biocommons/bioutils ↗

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