{"id":45933,"library":"python-codon-tables","title":"Codon Usage Tables for Python","description":"Provides codon usage tables for hundreds of organisms, sourced from Kazusa (https://www.kazusa.or.jp/codon/). Version 0.1.18 is the latest. Development is slow; no recent breaking changes.","status":"active","version":"0.1.18","language":"python","source_language":"en","source_url":"https://github.com/Edinburgh-Genome-Foundry/python_codon_tables","tags":["codon","usage","tables","biology"],"install":[{"cmd":"pip install python-codon-tables","lang":"bash","label":"Default"}],"dependencies":[],"imports":[{"wrong":"from codon_tables import get_codons_table","symbol":"get_codons_table","correct":"from python_codon_tables import get_codons_table"},{"symbol":"available_codon_tables_names","correct":"from python_codon_tables import available_codon_tables_names"},{"symbol":"get_all_available_codons_tables","correct":"from python_codon_tables import get_all_available_codons_tables"}],"quickstart":{"code":"from codon_tables import get_codons_table\n\ntable = get_codons_table('9606')  # Homo sapiens (Taxonomy ID 9606)\nprint(table['T'])  # codon TTT? Actually keys are codons\nprint(table['TTT'])  # Should be 0.58 or similar","lang":"python","description":"Fetch codon usage table for a taxonomy ID."},"warnings":[{"fix":"Always pass taxonomy ID as a string, e.g., '9606', or use str() when converting.","message":"Taxonomy IDs are integers but often used as strings; mixed usage may cause KeyError.","severity":"gotcha","affected_versions":"all"},{"fix":"If a specific strain is needed, use the exact taxonomy ID or consider an alternative source.","message":"Some species have multiple tables (different strains). The function returns only one; check table sources.","severity":"gotcha","affected_versions":"all"}],"env_vars":null,"search_vec":"'/codon/).':19 '0.1.18':21 'biolog':35 'break':30 'chang':31 'codon':1,7,32 'develop':25 'hundr':11 'kazusa':16 'latest':24 'organ':13 'provid':6 'python':5 'recent':29 'slow':27 'sourc':14 'tabl':3,9,34 'usag':2,8,33 'version':20 'www.kazusa.or.jp':18 'www.kazusa.or.jp/codon/).':17","created_at":"2026-06-07T12:57:27.298366+00:00","updated_at":"2026-06-07T12:57:27.298366+00:00","problems":null,"ecosystem":"pypi","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":null,"cli_name":null,"cli_version":null,"type":"library","homepage":"https://github.com/Edinburgh-Genome-Foundry/python_codon_tables","github":"https://github.com/Edinburgh-Genome-Foundry/python_codon_tables","docs":null,"changelog":null,"pypi":null,"npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["ai-ml"],"base_url":null,"auth_type":null,"provenance":{"verified_status":"passing","verified_at":"2026-07-03","last_verified":"2026-07-03","next_check":"2026-08-02","install_tag":null}}