{"id":21466722,"url":"https://github.com/edinburgh-genome-foundry/genedom","last_synced_at":"2025-07-23T11:07:52.750Z","repository":{"id":57433473,"uuid":"129428769","full_name":"Edinburgh-Genome-Foundry/genedom","owner":"Edinburgh-Genome-Foundry","description":"Batch domestication of genetic parts with Python","archived":false,"fork":false,"pushed_at":"2025-05-12T14:14:27.000Z","size":2629,"stargazers_count":16,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-07-15T09:03:07.304Z","etag":null,"topics":["dna-assembly","part-domestication","sequence-design","synbio","synthetic-biology"],"latest_commit_sha":null,"homepage":"https://edinburgh-genome-foundry.github.io/genedom/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Edinburgh-Genome-Foundry.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-04-13T16:37:54.000Z","updated_at":"2025-05-12T14:02:12.000Z","dependencies_parsed_at":"2025-07-15T05:31:19.243Z","dependency_job_id":"7603a46d-b5f9-4180-9a1d-affbbf0be252","html_url":"https://github.com/Edinburgh-Genome-Foundry/genedom","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/Edinburgh-Genome-Foundry/genedom","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fgenedom","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fgenedom/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fgenedom/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fgenedom/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Edinburgh-Genome-Foundry","download_url":"https://codeload.github.com/Edinburgh-Genome-Foundry/genedom/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fgenedom/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266665813,"owners_count":23964974,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-23T02:00:09.312Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["dna-assembly","part-domestication","sequence-design","synbio","synthetic-biology"],"created_at":"2024-11-23T08:15:03.235Z","updated_at":"2025-07-23T11:07:52.719Z","avatar_url":"https://github.com/Edinburgh-Genome-Foundry.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":".. raw:: html\n\n    \u003cp align=\"center\"\u003e\n    \u003cimg alt=\"logo\" title=\"Genedom Logo\" src=\"https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/genedom/master/docs/_static/images/logo.png\" width=\"550\"\u003e\n    \u003cbr /\u003e\u003cbr /\u003e\n    \u003c/p\u003e\n\n.. image:: https://github.com/Edinburgh-Genome-Foundry/genedom/actions/workflows/build.yml/badge.svg\n    :target: https://github.com/Edinburgh-Genome-Foundry/genedom/actions/workflows/build.yml\n    :alt: GitHub CI build status\n\n.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/genedom/badge.svg?branch=master\n  :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/genedom?branch=master\n\n\n\nGenedom is a Python package for managing the domestication of genetic parts,\nwhich means modifying their sequences to make them compatible with a given\ngenetic assembly standard. Genedom binds together a\n`sequence optimizer \u003chttps://github.com/Edinburgh-Genome-Foundry/DnaChisel\u003e`_,\ninformation on the genetic standard, and a reporting routine to automate the\ndomestication of large batches in an easy and human-friendly way.\n\n.. raw:: html\n\n    \u003cp align=\"center\"\u003e\n    \u003cimg alt=\"schema\" title=\"schema\" src=\"https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/genedom/master/docs/_static/images/domestication_schema.png\" width=\"800\"\u003e\n    \u003cbr /\u003e\u003cbr /\u003e\n    \u003c/p\u003e\n\nFeatures include:\n\n- User-defined part domesticators with extra nucleotides optionally added to both ends,\n  hard constraints on the sequence (such as enforcing absence of a restriction\n  site) and optimization objectives (such as codon optimization).\n- Built-in pre-defined domesticators for popular genetic assembly standards\n  (well, only EMMA at the moment).\n- Generation of barcodes that can be added to the sequence\n  (but won't be in final constructs). This allows easy verification of a sequence file\n  or a DNA sample (e.g. in case of label mix-up).\n- Routine for batch-domesticating sequences with report generation, including\n  reports on each sequence optimization, spreadsheets of parts, ready-to-order FASTA\n  and Genbank files of the parts, and a summary report to quickly verify everything,\n  with a list of every domesticator used, for traceability.\n\nAn example summary report:\n\n.. raw:: html\n\n    \u003cp align=\"center\"\u003e\n    \u003cimg alt=\"report\" title=\"report\" src=\"https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/genedom/master/docs/_static/images/report_screenshot.png\" width=\"600\"\u003e\n    \u003cbr /\u003e\u003cbr /\u003e\n    \u003c/p\u003e\n\n\nYou can also use Genedom online via EGF's `Domesticate Part Batches web app \u003chttps://cuba.genomefoundry.org/domesticate_part_batches\u003e`_.\n\nUsage examples\n--------------\n\nSimple domestication of one part\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code:: python\n\n    from genedom import (GoldenGateDomesticator, random_dna_sequence,\n                         write_record)\n    sequence = random_dna_sequence(2000, seed=123)\n    domesticator = GoldenGateDomesticator(\"ATTC\", \"ATCG\", enzyme='BsmBI')\n    domestication_results = domesticator.domesticate(sequence, edit=True)\n    print (domestication_results.summary())\n    write_record(domestication_results.record_after, 'domesticated.gb')\n\n\nGenerating a collection of 20bp barcodes\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n(see docs for more options)\n\n.. code:: python\n\n    from genedom import BarcodesCollection\n\n    barcodes_collection = BarcodesCollection.from_specs(\n        n_barcodes=96, barcode_length=20,\n        forbidden_enzymes=('BsaI', 'BsmBI', 'BbsI'))\n\n    barcodes_collection.to_fasta('example_barcodes_collection.fa')\n\n\nDomesticating a batch of parts with PDF report\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code:: python\n\n    from genedom import BUILTIN_STANDARDS, load_record, batch_domestication\n\n    records = [\n        load_record(filepath, name=filename)\n        for filepath in records_filepaths\n    ]\n    barcodes_collection = BarcodesCollection.from_specs(n_barcodes=10)\n    batch_domestication(records, 'domestication_report.zip',\n                        barcodes=barcodes,  # optional\n                        standard=BUILTIN_STANDARDS.EMMA)\n\n\nInstallation\n------------\n\nYou can install Genedom through PIP:\n\n.. code:: shell\n\n    pip install genedom\n\n\nLicense = MIT\n-------------\n\nGenedom is a free/libre and open-source software\n`released on Github \u003chttps://github.com/Edinburgh-Genome-Foundry/genedom\u003e`_ under\nthe MIT license (Copyright 2018 Edinburgh Genome Foundry, University of Edinburgh).\nIt was originally written by `Zulko \u003chttps://github.com/Zulko\u003e`_ and is currently\nbeing developed by `Peter Vegh \u003chttps://github.com/veghp\u003e`_.\nEveryone is welcome to `contribute \u003chttps://github.com/Edinburgh-Genome-Foundry/HowTo/blob/master/EGF/CONTRIBUTING.md\u003e`_!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedinburgh-genome-foundry%2Fgenedom","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fedinburgh-genome-foundry%2Fgenedom","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedinburgh-genome-foundry%2Fgenedom/lists"}