{"id":23051533,"url":"https://github.com/averissimo/gene-extractor","last_synced_at":"2026-07-09T19:31:43.110Z","repository":{"id":20936396,"uuid":"24224683","full_name":"averissimo/gene-extractor","owner":"averissimo","description":"Searchs independent search term against KEGG and GeneBank (NCBI)","archived":false,"fork":false,"pushed_at":"2015-06-25T15:13:14.000Z","size":292,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-03T04:15:13.652Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Ruby","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/averissimo.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":"2014-09-19T09:44:39.000Z","updated_at":"2015-02-10T16:26:09.000Z","dependencies_parsed_at":"2022-08-17T16:01:30.126Z","dependency_job_id":null,"html_url":"https://github.com/averissimo/gene-extractor","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/averissimo/gene-extractor","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Fgene-extractor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Fgene-extractor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Fgene-extractor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Fgene-extractor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/averissimo","download_url":"https://codeload.github.com/averissimo/gene-extractor/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Fgene-extractor/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35311290,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-09T02:00:07.329Z","response_time":57,"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":[],"created_at":"2024-12-15T23:46:17.556Z","updated_at":"2026-07-09T19:31:43.088Z","avatar_url":"https://github.com/averissimo.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"GeneExtractor\n==============\n\nSearchs independent terms against different databases and retrieves gene sequences from:\n- KEGG - [link](http://www.genome.jp/kegg/genes.html)\n- NCBI Nucleotide - [link](http://www.ncbi.nlm.nih.gov/nuccore/)\n\n## Requirements\n\n- [Ruby runtime environment](https://www.ruby-lang.org/en/installation/)\n - [Windows](http://rubyinstaller.org/)\n - [Mac OSX and Linux](http://rvm.io/)\n- Bundle Gem - `gem install bundle`\n- [Bioruby gem](http://www.bioruby.org)\n\n## How to Use\n\n1. Run `bundle install --path vendor/bundle` to install dependencies *(currently only Bioruby)*\n1. Create a `keys.txt` file *(either by copying keys.txt.example or creating a blank one)*\n - Add query terms to keys.txt *(separated by new lines)*\n1. Create a `config.yml` file *(either by copying keys.txt.example or creating a blank one)*\n - Open the file and change options (if need be)\n1. Run `bundle exec ruby script.rb` to search and download all the associated genes\n - If you don't install gems locally then just run `ruby script.rb`\n\n### Config.yml options\n\nYML syntax is used to configure GeneExtractor. It is an hierarchical file that uses indentation to define children attribute or lists.\n\n- *email*: user's valid email address necessary to use NCBI Rest API\n- *output*:\n - *dir*: parent folder to place results from GeneExtractor\n - *data_prefix*: add an additional fodler level with date and time when GeneExtractor was executed\n - *kegg*: folder name for kegg results\n - *ncbi*: folder name for ncbi results\n- *search*:\n - *ncbi*: list of fields that should be searched in NCBI (each field)\n\n#### example config.yml\n\n    email: gene.extractor@mailinator.com\n    output:\n      dir: queries\n      date_prefix: true\n      kegg: kegg\n      ncbi: ncbi\n\n    search:\n      ncbi:\n        - Protein name\n        - Gene name\n        - Title\n\n\n## Ackowledgements\n\nThis tool was created as a part of [FCT](www.fct.p) grant SFRH/BD/97415/2013 and European Commission research project [BacHBerry](www.bachberry.eu) (FP7- 613793)\n\n[Developer](http://web.tecnico.ulisboa.pt/andre.verissimo/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faverissimo%2Fgene-extractor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faverissimo%2Fgene-extractor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faverissimo%2Fgene-extractor/lists"}