bioutils

0.6.1 verified Fri May 01 auth: no python

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.

pip install bioutils

Common errors

error AttributeError: module 'bioutils' has no attribute 'codons' ↓

cause Trying to access bioutils.codons after import bioutils, but submodules need explicit import.

fix

Use 'from bioutils import codons' instead of 'import bioutils' then 'bioutils.codons'.

error ImportError: cannot import name 'translate' from 'bioutils' ↓

cause The correct import is from bioutils.codons, not from bioutils directly.

fix

Use 'from bioutils.codons import translate'.

Warnings

breaking Version 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.

gotcha Functions 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.

Imports

codons
wrong
```
import bioutils.codons
```
correct
```
from bioutils import codons
```
bioutils.codons is a module, but direct import will fail unless using bioutils as a package
sequences
wrong
```
import bioutils.sequences
```
correct
```
from bioutils import sequences
```
Same as above; must use explicit from import

Quickstart

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)