{"id":19434524,"url":"https://github.com/mlin/genomicsqlite-examples","last_synced_at":"2025-10-08T11:45:10.326Z","repository":{"id":138431192,"uuid":"352226036","full_name":"mlin/GenomicSQLite-examples","owner":"mlin","description":null,"archived":false,"fork":false,"pushed_at":"2021-03-30T00:52:32.000Z","size":9,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-01-07T20:46:11.684Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","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/mlin.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":"2021-03-28T02:45:05.000Z","updated_at":"2021-03-30T00:52:34.000Z","dependencies_parsed_at":null,"dependency_job_id":"71694eef-9614-40ff-893c-70a7c04d633e","html_url":"https://github.com/mlin/GenomicSQLite-examples","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/mlin%2FGenomicSQLite-examples","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FGenomicSQLite-examples/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FGenomicSQLite-examples/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FGenomicSQLite-examples/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mlin","download_url":"https://codeload.github.com/mlin/GenomicSQLite-examples/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240614778,"owners_count":19829408,"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":[],"created_at":"2024-11-10T14:46:42.443Z","updated_at":"2025-10-08T11:45:05.261Z","avatar_url":"https://github.com/mlin.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GenomicSQLite-examples\n\nThis repo exhibits a simple example program using [Genomics Extension for SQLite](https://github.com/mlin/GenomicSQLite), implemented in several supported programming languages. It's a minimal starting point to fork into your own program. See the [Programming Guide](https://mlin.github.io/GenomicSQLite) for full documentation.\n\nEach implementation provides two subcommands:\n\n1. `gsqlex load exons.gff exons.db` imports a small [GFF file](https://en.wikipedia.org/wiki/General_feature_format) into a new database, indexed by genomic range\n2. `gsqlex query exons.db chr17:43,104,800-43,105,000` prints the records overlapping the given genomic range\n\nGeneral requirements: x86-64, Linux or macOS, installed development package for SQLite 3.31.0+.\n\n### Python (3.6+)\n\n```\npip3 install genomicsqlite\n\ngit clone https://github.com/mlin/GenomicSQLite-examples.git\ncd GenomicSQLite-examples/python\n\npython3 gsqlex.py load ../exons.gff exons.db\npython3 gsqlex.py query exons.db chr17:43,104,800-43,105,000\n```\n\n### C\n\n```\ngit clone https://github.com/mlin/GenomicSQLite-examples.git\ncd GenomicSQLite-examples/c\n\nwget https://github.com/mlin/GenomicSQLite/releases/download/v0.8.0/GenomicSQLite-v0.8.0.zip\nunzip GenomicSQLite-v0.8.0.zip\n\ncc -o gsqlex -L$(pwd) gsqlex.c -lsqlite3 -lgenomicsqlite -Wl,-rpath,\\$ORIGIN\n\n./gsqlex load ../exons.gff exons.db\n./gsqlex query exons.db chr17:43,104,800-43,105,000\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlin%2Fgenomicsqlite-examples","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmlin%2Fgenomicsqlite-examples","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlin%2Fgenomicsqlite-examples/lists"}