{"id":25268900,"url":"https://github.com/sgelias/abiorganizer","last_synced_at":"2025-04-06T04:41:02.180Z","repository":{"id":57407727,"uuid":"240978848","full_name":"sgelias/AbiOrganizer","owner":"sgelias","description":"Extract and distribute ab1 files from Sanger DNA sequencing to folders of their respective owners.","archived":false,"fork":false,"pushed_at":"2020-07-12T21:34:11.000Z","size":6,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-14T04:21:54.175Z","etag":null,"topics":["ab1-organizer","primer","sanger-chromatograms","sanger-sequencing"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sgelias.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-02-16T22:52:01.000Z","updated_at":"2020-08-16T18:39:37.000Z","dependencies_parsed_at":"2022-09-26T17:10:43.226Z","dependency_job_id":null,"html_url":"https://github.com/sgelias/AbiOrganizer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sgelias%2FAbiOrganizer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sgelias%2FAbiOrganizer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sgelias%2FAbiOrganizer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sgelias%2FAbiOrganizer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sgelias","download_url":"https://codeload.github.com/sgelias/AbiOrganizer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247436143,"owners_count":20938532,"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":["ab1-organizer","primer","sanger-chromatograms","sanger-sequencing"],"created_at":"2025-02-12T10:39:12.367Z","updated_at":"2025-04-06T04:41:02.154Z","avatar_url":"https://github.com/sgelias.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ab1_organizer\n\n## Goal\n\nOrganize AB1 files by researches and primer-pairs.\n\n## Instalation\n\nFor command line usage, simpleously use pip way:\n\n```bash\n\npip install ab1_organizer\n\n```\n\n## Usage\n\n`ab1_organizer` receive two arguments on initialization: the results file from Macrogen sequencing (-f, --file argument) and the modified order table (-t, --table argument). The sequencing file consists of the raw zipfile (file-name.zip) containing all .ab1, .pdf, phd.1, and .txt files. The order file consists of a simple excel table containing Macrogen order specifications and containing standardized headers (see next section).\n\n### Standardized headers\n\nYour table would contain almost four columns, named respectively:\n- sampleName: The unique identifier of sample;\n- primerName: The primer name. e.g. \"CO3 F\", or \"ITS1 R\";\n- personInCharge: The name of a person or a project responsible for the sample processing;\n- primerCombination: Underscore separated complementary primer names. As example, if some region are sequenced using the \"ITS1-F\" and \"ITS1-R\", the primerCombination would be \"ITS1-F_ITS1-R\".\n\n\nAt the terminal, run the code:\n\n```bash\n\nab1_organizer.py -f ./path/to/zip/file -t ./path/to/order/table.xlsx\n\n```\n\nA new folder with the same name of the zip file will be created and all files will be organized by author and genomic marker respectively.\n\n\n```bash\n\n./190731FN-022/\n├── person1\n│   ├── ITS1-F_ITS1-R\n│   │   ├── 01_ITS1-F.ab1\n│   │   ├── 01_ITS1-F.pdf\n│   │   ├── 01_ITS1-F.phd.1\n│   │   ├── 01_ITS1-F.txt\n│   │   ├── 01_ITS1-R.ab1\n│   │   ├── 01_ITS1-R.pdf\n│   │   ├── 01_ITS1-R.phd.1\n│   │   ├── 01_ITS1-R.txt\n├── person2\n│   ├── ITS1-F_ITS1-R\n│   │   ├── 01_ITS1-F.ab1\n│   │   ├── 01_ITS1-F.pdf\n│   │   ├── 01_ITS1-F.phd.1\n│   │   ├── 01_ITS1-F.txt\n│   │   ├── 01_ITS1-R.ab1\n│   │   ├── 01_ITS1-R.pdf\n│   │   ├── 01_ITS1-R.phd.1\n│   │   ├── 01_ITS1-R.txt\n...\n\n```\n\n\n---\n\nFeel free to add new features and contribute through pull requests. Be happy!!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsgelias%2Fabiorganizer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsgelias%2Fabiorganizer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsgelias%2Fabiorganizer/lists"}