{"id":19857011,"url":"https://github.com/griffithlab/civic2clinvar","last_synced_at":"2025-07-16T11:09:26.138Z","repository":{"id":62562360,"uuid":"129626700","full_name":"griffithlab/civic2clinvar","owner":"griffithlab","description":"extraction of CIViC variants into the clinvar submission format","archived":false,"fork":false,"pushed_at":"2019-04-02T01:43:41.000Z","size":12,"stargazers_count":1,"open_issues_count":1,"forks_count":1,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-06-25T23:38:11.330Z","etag":null,"topics":["civic"],"latest_commit_sha":null,"homepage":null,"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/griffithlab.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}},"created_at":"2018-04-15T16:02:57.000Z","updated_at":"2024-02-02T04:37:24.000Z","dependencies_parsed_at":"2022-11-03T15:17:42.925Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/civic2clinvar","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/griffithlab/civic2clinvar","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic2clinvar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic2clinvar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic2clinvar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic2clinvar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/civic2clinvar/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic2clinvar/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261973305,"owners_count":23238548,"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":["civic"],"created_at":"2024-11-12T14:17:12.068Z","updated_at":"2025-06-25T23:38:22.759Z","avatar_url":"https://github.com/griffithlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# civic2clinvar\n\n`civic2clinvar` is a python-based command line utility for extracting [CIViC](https://civicdb.org) assertions and translating them into ClinVar records.\n\n## Installation\n`$ pip install civic2clinvar`\n\n## Usage\n```\n$ civic2clinvar --help\n\nUsage: civic2clinvar [OPTIONS] ASSERTION_IDS\n\n  This command generates a ClinVar-formatted csv file from a specified set\n  of CIViC assertions.\n\n  ASSERTION_IDS are a comma-separated list of assertions, and accepts\n  integer ranges. Example usage:\n\n  civic2clinvar 1,3-5\n\n  The above command outputs a ClinVar submission form describing CIViC\n  assertions 1, 3, 4, and 5 to clinvar.csv (the default output file). Output\n  destination may be controlled with the --out option, detailed below.\n\n  CIViC assertions that are rejected or pending are skipped.\n\nOptions:\n  --aid-file FILENAME  Optional file of newline-separated assertion IDs. This\n                       option is mutually exclusive with the ASSERTION_IDS\n                       argument.\n  -o, --out FILENAME   Output file (default: clinvar.csv), use '-' for STDOUT\n  --help               Show this message and exit.\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic2clinvar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fcivic2clinvar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic2clinvar/lists"}