{"id":23362,"library":"bioutils","title":"bioutils","description":"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.","status":"active","version":"0.6.1","language":"python","source_language":"en","source_url":"https://github.com/biocommons/bioutils","tags":["bioinformatics","codon-translation","sequence-utilities","assembly","biocommons"],"install":[{"cmd":"pip install bioutils","lang":"bash","label":"Default install"}],"dependencies":[{"reason":"Required for sequence I/O and biological sequence objects","package":"biopython","optional":false},{"reason":"Used for online assembly lookups and NCBI API calls","package":"requests","optional":false}],"imports":[{"note":"bioutils.codons is a module, but direct import will fail unless using bioutils as a package","wrong":"import bioutils.codons","symbol":"codons","correct":"from bioutils import codons"},{"note":"Same as above; must use explicit from import","wrong":"import bioutils.sequences","symbol":"sequences","correct":"from bioutils import sequences"}],"quickstart":{"code":"from bioutils import codons, sequences\n\n# Translate a DNA sequence to protein\ndna = \"ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG\"\nprotein = codons.translate(dna)\nprint(protein)\n\n# Get reverse complement\nrev_comp = sequences.reverse_complement(dna)\nprint(rev_comp)","lang":"python","description":"Demonstrates basic codon translation and sequence manipulation."},"warnings":[{"fix":"Upgrade to Python >=3.10 or pin bioutils to <0.6.0.","message":"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.","severity":"breaking","affected_versions":">=0.6.0"},{"fix":"Convert Seq objects to string using str(seq) before passing to bioutils functions.","message":"Functions like codons.translate() and sequences.reverse_complement() expect plain string input, not Bio.Seq objects. Passing a Seq object will cause a TypeError.","severity":"gotcha","affected_versions":"all"}],"env_vars":null,"last_verified":"2026-05-01T00:00:00.000Z","next_check":"2026-07-30T00:00:00.000Z","problems":[{"fix":"Use 'from bioutils import codons' instead of 'import bioutils' then 'bioutils.codons'.","cause":"Trying to access bioutils.codons after import bioutils, but submodules need explicit import.","error":"AttributeError: module 'bioutils' has no attribute 'codons'"},{"fix":"Use 'from bioutils.codons import translate'.","cause":"The correct import is from bioutils.codons, not from bioutils directly.","error":"ImportError: cannot import name 'translate' from 'bioutils'"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}