{"id":15384683,"url":"https://github.com/bblodfon/rsat-rest-java-clients","last_synced_at":"2025-07-29T00:34:20.240Z","repository":{"id":90675312,"uuid":"183593778","full_name":"bblodfon/rsat-rest-java-clients","owner":"bblodfon","description":"Java Clients for the Regulatory Sequence Analysis Tools (RSAT) REST API","archived":false,"fork":false,"pushed_at":"2019-04-26T08:54:58.000Z","size":23,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-07T19:00:11.167Z","etag":null,"topics":["genome-analysis","java-8","regulation"],"latest_commit_sha":null,"homepage":null,"language":"Java","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/bblodfon.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-04-26T08:53:36.000Z","updated_at":"2019-04-26T14:13:08.000Z","dependencies_parsed_at":null,"dependency_job_id":"4ffdd048-058f-4fa3-8a1e-723f93f97fec","html_url":"https://github.com/bblodfon/rsat-rest-java-clients","commit_stats":{"total_commits":2,"total_committers":1,"mean_commits":2.0,"dds":0.0,"last_synced_commit":"93e2e5a29243cd3b0d40f0dccf8c722d60e5cadc"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bblodfon/rsat-rest-java-clients","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Frsat-rest-java-clients","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Frsat-rest-java-clients/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Frsat-rest-java-clients/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Frsat-rest-java-clients/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bblodfon","download_url":"https://codeload.github.com/bblodfon/rsat-rest-java-clients/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Frsat-rest-java-clients/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267610438,"owners_count":24115435,"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","status":"online","status_checked_at":"2025-07-28T02:00:09.689Z","response_time":68,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["genome-analysis","java-8","regulation"],"created_at":"2024-10-01T14:43:04.026Z","updated_at":"2025-07-29T00:34:20.201Z","avatar_url":"https://github.com/bblodfon.png","language":"Java","readme":"# rsat-rest-java-clients\n\nThis module is a Java Client for the Regulatory Sequence Analysis Tools (RSAT) \n[RESTful API](http://rsat-tagc.univ-mrs.fr/rest/). \n\nCurrently, only one tool is supported with a Java Client, namely the \n`fetch-sequences` tool. This tool is used to retrieve genome sequences for a \nset of coordinates specified in a bed file (either from a resource URL through \nthe `GET` and `POST` methods or from a local .bed file through `POST`).\n\n## Install\n\nTested with maven version 3.6.0, compiled with Java 8\n```\nmvn clean install\n```\n\n## Examples\n\n- When using no arguments, you get the list of available parameters:\n```\njava -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient \n\nOptions preceded by an asterisk are required.\nUsage: clients.FetchSequencesClient [options]\n  Options:\n  * --requestMethod, -m\n      The HTTP request method: GET or POST\n    --responseContentType, -c\n      The response content type: json or text\n      Default: json\n    --genome, -g\n      Genome version (e.g. mm9, hg19)\n      Default: mm9\n    --header, -h\n      Format for sequence headers: UCSC or galaxy\n      Default: galaxy\n    --resourceURL, -u\n      URL file resource\n    --resourceBedFile, -f\n      File in .bed format\n```\n\n- Using the `GET` HTTP method to retrieve the sequences from a URL resource:\n```\njava -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient -m=GET -c=json -u=http://rsat-tagc.univ-mrs.fr/rsat/demo_files/fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks.bed -g=mm9 -h=galaxy\n```\n\n- Using the `POST` HTTP method to retrieve the sequences from a URL resource:\n```\njava -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient -m=POST -c=text -u=http://rsat-tagc.univ-mrs.fr/rsat/demo_files/fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks.bed -g=mm9 -h=galaxy\n```\n\n- Using the `POST` HTTP method to retrieve the sequences from a local .bed file \nresource:\n```\njava -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient -m=POST -c=json -f=src/main/resources/test.bed -g=mm9 -h=galaxy\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbblodfon%2Frsat-rest-java-clients","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbblodfon%2Frsat-rest-java-clients","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbblodfon%2Frsat-rest-java-clients/lists"}