{"id":47839979,"url":"https://github.com/barricklab/widespread-recurrent-part-variants","last_synced_at":"2026-04-03T20:36:52.419Z","repository":{"id":185235061,"uuid":"625030008","full_name":"barricklab/widespread-recurrent-part-variants","owner":"barricklab","description":"Analysis code for identifying genetic part variants in engineered plasmids","archived":false,"fork":false,"pushed_at":"2023-04-20T17:36:48.000Z","size":459,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-09T13:54:10.377Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/barricklab.png","metadata":{"files":{"readme":"README.md","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}},"created_at":"2023-04-07T21:57:01.000Z","updated_at":"2023-04-20T16:50:46.000Z","dependencies_parsed_at":"2023-08-01T07:09:12.918Z","dependency_job_id":null,"html_url":"https://github.com/barricklab/widespread-recurrent-part-variants","commit_stats":null,"previous_names":["barricklab/widespread-recurrent-part-variants"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/barricklab/widespread-recurrent-part-variants","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2Fwidespread-recurrent-part-variants","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2Fwidespread-recurrent-part-variants/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2Fwidespread-recurrent-part-variants/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2Fwidespread-recurrent-part-variants/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/barricklab","download_url":"https://codeload.github.com/barricklab/widespread-recurrent-part-variants/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2Fwidespread-recurrent-part-variants/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31375772,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-03T17:53:18.093Z","status":"ssl_error","status_checked_at":"2026-04-03T17:53:17.617Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2026-04-03T20:36:51.802Z","updated_at":"2026-04-03T20:36:52.400Z","avatar_url":"https://github.com/barricklab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/625030008.svg)](https://zenodo.org/badge/latestdoi/625030008)\n\nAnalysis code for:\n\nMcGuffie, M.J., Barrick, J.E., 2023. __Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences.__ https://doi.org/10.1101/2023.04.10.536277\n\nThis code uses a directory of CSVs generated by [pLannotate](https://github.com/barricklab/pLannotate) v1.2.0 from the Addgene plasmid database as input. The Addgene plasmid IDs used in analysis are available at [`data/addgene_ids.txt.gz`](./data/addgene_ids.txt.gz) in this repository. The associated plasmid sequences are available individually from the AddGene website (https://www.addgene.org/browse/) for download, and available for bulk download from AddGene upon request.\n\nThe computational enviroment can be created using the provided `env.yml` file with [conda](https://docs.conda.io/en/latest/) or [mamba](https://mamba.readthedocs.io/en/latest/installation.html). The environment can be created with the following command:\n\n```bash\nmamba env create -f env.yml\n```\n\n1. Annotate plasmids with pLannotate and output the results to a directory of CSVs.\n2. Run `01_parsing_annotate_addgene_csvs.ipynb` to collect and clean the data.\n3. Run `02_pairwise_ds_scores.py` to calculate DS scores of plasmid pairs.\n4. Run `03_analyzing_clusters.ipynb` to cluster and analyze the part variants.\n\nThe output CSV of identified variants is available at [`data/supplemental_table_1.csv.gz`](./data/supplemental_table_1.csv.gz) in this repository.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbarricklab%2Fwidespread-recurrent-part-variants","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbarricklab%2Fwidespread-recurrent-part-variants","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbarricklab%2Fwidespread-recurrent-part-variants/lists"}