{"id":19577752,"url":"https://github.com/therook/multiplexedplasmidbuilder","last_synced_at":"2026-06-13T11:33:27.067Z","repository":{"id":148890678,"uuid":"604330058","full_name":"TheRook/MultiplexedPlasmidBuilder","owner":"TheRook","description":"To combine and modify genbank files to construct multiplexed CRISPR plasmids.","archived":false,"fork":false,"pushed_at":"2023-02-20T21:27:26.000Z","size":19,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-09T04:46:18.057Z","etag":null,"topics":["biohacking","biology","biopython","crispr","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/TheRook.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":"2023-02-20T20:40:18.000Z","updated_at":"2023-07-18T09:23:02.000Z","dependencies_parsed_at":"2023-07-17T02:01:50.760Z","dependency_job_id":null,"html_url":"https://github.com/TheRook/MultiplexedPlasmidBuilder","commit_stats":{"total_commits":8,"total_committers":1,"mean_commits":8.0,"dds":0.0,"last_synced_commit":"346d565cdf5bc0d44283ca51e9cd873e38638c14"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TheRook%2FMultiplexedPlasmidBuilder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TheRook%2FMultiplexedPlasmidBuilder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TheRook%2FMultiplexedPlasmidBuilder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TheRook%2FMultiplexedPlasmidBuilder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/TheRook","download_url":"https://codeload.github.com/TheRook/MultiplexedPlasmidBuilder/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240848985,"owners_count":19867615,"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","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":["biohacking","biology","biopython","crispr","python"],"created_at":"2024-11-11T07:08:02.806Z","updated_at":"2026-06-13T11:33:27.013Z","avatar_url":"https://github.com/TheRook.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Construct a Multiplexed Plasmid\nThis project simplifies the process of building multiplexed-plasmids and packaging them up into a single annoated genbank file that can be easily used on benchling or another workbench.  Although this task is commonly perfomred by hand in a browser or desktop application, performing senstive tasks like this with python allows us to be eaxct with our changes and to verify the changes.\n\n### CLI Input\nThe script accepts the following input parameters:\n\n- --backbone-file: Required. The path to the GenBank file of the plasmid backbone to build from.\n- --target-dir: Required. The path to the directory containing the list of target genes to replace.\n- --replacement-dir: Required. The path to the directory containing the list of replacement genes to use.\n- --crispr-file: Required. The path to the GenBank file containing the desired multiplexed-CRISPR variant.\n- --output-file: Required. The path to the final plasmid.\n\n\n### Example Usage\nTo use the script, navigate to the directory containing the script and run the following command:\n\n`python3 main.py --backbone-file ./genes/backbone.gb --target-dir ./genes/targets/ --replacement-dir ./genes/replacements/ --crispr-file ./genes/crispr.gb --output-file plasmid_1.gb`\n\nThis command assumes CRISPR is being used for a 1:1 replacment of a list of genes. To do this the code above will modify the plasmid GenBank file located at genes/backbone.gb and will add pair the replacements with targets based off of the alphabetical sort order of both directories.\n\n### Reproduceablity / Flexablity\nCommands can be saved within a .sh file and re-run to re-build a specific plasmid when needed. A team should be able to build any number of therapies or tests out of the same directory.  The code will take in fasta or genebank files.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftherook%2Fmultiplexedplasmidbuilder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftherook%2Fmultiplexedplasmidbuilder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftherook%2Fmultiplexedplasmidbuilder/lists"}