{"id":21845873,"url":"https://github.com/abhijeetsingh1704/proteincleaner","last_synced_at":"2025-03-21T16:42:15.373Z","repository":{"id":68618864,"uuid":"497363581","full_name":"abhijeetsingh1704/PROTEINcleaner","owner":"abhijeetsingh1704","description":"a python utility to clean PROTEIN sequences and headers","archived":false,"fork":false,"pushed_at":"2022-05-28T16:04:22.000Z","size":7,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-26T12:09:47.634Z","etag":null,"topics":["convertion","fasta","genbank"],"latest_commit_sha":null,"homepage":"","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/abhijeetsingh1704.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-05-28T15:56:51.000Z","updated_at":"2022-08-11T00:44:17.000Z","dependencies_parsed_at":"2023-09-13T17:26:19.096Z","dependency_job_id":null,"html_url":"https://github.com/abhijeetsingh1704/PROTEINcleaner","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/abhijeetsingh1704%2FPROTEINcleaner","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abhijeetsingh1704%2FPROTEINcleaner/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abhijeetsingh1704%2FPROTEINcleaner/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abhijeetsingh1704%2FPROTEINcleaner/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/abhijeetsingh1704","download_url":"https://codeload.github.com/abhijeetsingh1704/PROTEINcleaner/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244830750,"owners_count":20517557,"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":["convertion","fasta","genbank"],"created_at":"2024-11-27T23:11:42.734Z","updated_at":"2025-03-21T16:42:15.346Z","avatar_url":"https://github.com/abhijeetsingh1704.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PROTEINcleaner\na python utility to clean PROTEIN sequences and headers\n\n```\nusage: PROTEINcleaner [-h] -i INPUT [-f INPUT_FORMAT] [-o OUTPUT]\n                      [-F OUTPUT_FORMAT] [-c Y/y or N/n] [-v Y/y or N/n] [-V]\n\nCleans invalid bases/residues in PROTEIN sequence file i.e., replaces invalid bases with Xs\n\nCitation: Singh, Abhijeet. PROTEINcleaner: a python utility to clean PROTEIN sequences and headers. \nResearchGate 2022, http://dx.doi.org/10.13140/RG.2.2.11468.49283, \nAvailable at GitHub: https://github.com/abhijeetsingh1704/PROTEINcleaner\n\nrequired arguments:\n  -i INPUT, --input INPUT\n                        input file\n\noptions:\n  -h, --help            show this help message and exit\n  -f INPUT_FORMAT, --input_format INPUT_FORMAT\n                        format of input file\n                        1 = fasta (default)\n                        2 = genbank\n  -o OUTPUT, --output OUTPUT\n                        output file (default: Clean\u003ctime\u003e_\u003cinput_file\u003e\u003c.ext\u003e)\n  -F OUTPUT_FORMAT, --output_format OUTPUT_FORMAT\n                        format of output fasta file\n                        1 = interleaved fasta (default)\n                        2 = fasta-2line\n                        3 = tab-delimited\n  -c Y/y or N/n, --clean_header Y/y or N/n\n                        clean and replace special characters in header\n                        with underscore \"_\" (default: N)\n  -v Y/y or N/n, --verbose Y/y or N/n\n                        print progress to the terminal (default: verbose)\n  -V, --version         show program's version number and exit\n\n```\n\n# Citation\nCitation: Singh, Abhijeet. PROTEINcleaner: a python utility to clean PROTEIN sequences and headers. ResearchGate 2022, http://dx.doi.org/10.13140/RG.2.2.11468.49283, Available at GitHub: https://github.com/abhijeetsingh1704/PROTEINcleaner\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabhijeetsingh1704%2Fproteincleaner","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fabhijeetsingh1704%2Fproteincleaner","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabhijeetsingh1704%2Fproteincleaner/lists"}