{"id":34733866,"url":"https://github.com/linzhi2013/msa_cigars","last_synced_at":"2026-04-01T22:39:33.209Z","repository":{"id":113363319,"uuid":"144555053","full_name":"linzhi2013/msa_cigars","owner":"linzhi2013","description":"A tool to get the CIGARs of a multiple sequence alignment.","archived":false,"fork":false,"pushed_at":"2021-09-23T13:03:52.000Z","size":35,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-26T14:01:00.780Z","etag":null,"topics":["alignment","biopython","cigars","msa"],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linzhi2013.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2018-08-13T09:04:39.000Z","updated_at":"2021-09-23T13:03:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"5e368a0b-7e9c-4496-9970-506a6dcfeb91","html_url":"https://github.com/linzhi2013/msa_cigars","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/linzhi2013/msa_cigars","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linzhi2013%2Fmsa_cigars","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linzhi2013%2Fmsa_cigars/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linzhi2013%2Fmsa_cigars/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linzhi2013%2Fmsa_cigars/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linzhi2013","download_url":"https://codeload.github.com/linzhi2013/msa_cigars/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linzhi2013%2Fmsa_cigars/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31013657,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-27T02:58:54.984Z","status":"ssl_error","status_checked_at":"2026-03-27T02:58:46.993Z","response_time":164,"last_error":"SSL_read: 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":["alignment","biopython","cigars","msa"],"created_at":"2025-12-25T03:20:36.384Z","updated_at":"2026-04-01T22:39:33.197Z","avatar_url":"https://github.com/linzhi2013.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# msa_cigars\n\n## 1 Introduction\n\n`msa_cigars` is a tool to get the CIGARs of a multiple sequence alignment. ONE alignment in the input file is assumed! CIGARs are in respect of the reference sequence. By Guanliang MENG, see https://github.com/linzhi2013/msa_cigars. \n\n## 2 Installation\n\n    pip install msa_cigars\n\nThere will be a command `msa_cigars` created under the same directory as your `pip` command.\n\n## 3 Usage\n    \n    $ msa_cigars\n    usage: msa_cigars [-h] -i \u003cFILE\u003e -refseq_id \u003cSTR\u003e [-n \u003cSTR\u003e] [-g \u003cSTR\u003e]\n                     [-f \u003cFORMAT\u003e] [-o \u003cFILE\u003e]\n\n        To get the CIGARs of a multiple sequence alignment.\n        ONE alignment in the input file is assumed!\n\n        CIGARs are in respect of the reference sequence.\n\n        'O' normal bases, e.g. A, T, G, C\n        '-' deletion\n        'N' unknown base\n\n            seq - - - N N N O O O\n         refseq - N O N - O O N -\n          cigar P n D B u U M N I\n\n        By Guanliang MENG,\n        see https://github.com/linzhi2013/msa_cigars.\n\n        optional arguments:\n          -h, --help        show this help message and exit\n          -i \u003cFILE\u003e         input msa file\n          -refseq_id \u003cSTR\u003e  MsaCigars class uses regular expression to find out the\n                            sequence id of refseq. Thus, make sure the value of\n                            'refseq_id' option is unique among the input msa file.\n          -n \u003cSTR\u003e          character of unknown base [N]\n          -g \u003cSTR\u003e          character of gap base [-]\n          -f \u003cFORMAT\u003e       the msa format [fasta]\n          -o \u003cFILE\u003e         outfile name [stdout]\n\n\n## 4 Author\nGuanliang MENG\n\n## 5 Citation\nCurrently I have no plan to publish `msa_cigars`. **However, if you use this program in your analysis, or you \"steal\" the idea/codes of this program into your script, I should be one of the co-authors in your publication!!!**\n\nHowever, since `msa_cigars` makes use of `Biopython`, you should also cite it if you use `breakSeqInNs_then_translate` in your work:\n\n    Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163\n\nPlease go to `http://www.biopython.org/` for more details.\n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinzhi2013%2Fmsa_cigars","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinzhi2013%2Fmsa_cigars","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinzhi2013%2Fmsa_cigars/lists"}