{"action":"created","issue":{"url":"https://api.github.com/repos/rockt/SETH/issues/6","repository_url":"https://api.github.com/repos/rockt/SETH","labels_url":"https://api.github.com/repos/rockt/SETH/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/rockt/SETH/issues/6/comments","events_url":"https://api.github.com/repos/rockt/SETH/issues/6/events","html_url":"https://github.com/rockt/SETH/issues/6","id":37465573,"number":6,"title":"Wrong mutation type recognized","user":{"login":"Erechtheus","id":3033565,"avatar_url":"https://avatars.githubusercontent.com/u/3033565?v=3","gravatar_id":"","url":"https://api.github.com/users/Erechtheus","html_url":"https://github.com/Erechtheus","followers_url":"https://api.github.com/users/Erechtheus/followers","following_url":"https://api.github.com/users/Erechtheus/following{/other_user}","gists_url":"https://api.github.com/users/Erechtheus/gists{/gist_id}","starred_url":"https://api.github.com/users/Erechtheus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Erechtheus/subscriptions","organizations_url":"https://api.github.com/users/Erechtheus/orgs","repos_url":"https://api.github.com/users/Erechtheus/repos","events_url":"https://api.github.com/users/Erechtheus/events{/privacy}","received_events_url":"https://api.github.com/users/Erechtheus/received_events","type":"User","site_admin":false},"labels":[{"id":21729947,"url":"https://api.github.com/repos/rockt/SETH/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":{"login":"rockt","id":1196835,"avatar_url":"https://avatars.githubusercontent.com/u/1196835?v=3","gravatar_id":"","url":"https://api.github.com/users/rockt","html_url":"https://github.com/rockt","followers_url":"https://api.github.com/users/rockt/followers","following_url":"https://api.github.com/users/rockt/following{/other_user}","gists_url":"https://api.github.com/users/rockt/gists{/gist_id}","starred_url":"https://api.github.com/users/rockt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rockt/subscriptions","organizations_url":"https://api.github.com/users/rockt/orgs","repos_url":"https://api.github.com/users/rockt/repos","events_url":"https://api.github.com/users/rockt/events{/privacy}","received_events_url":"https://api.github.com/users/rockt/received_events","type":"User","site_admin":false},"assignees":[{"login":"rockt","id":1196835,"avatar_url":"https://avatars.githubusercontent.com/u/1196835?v=3","gravatar_id":"","url":"https://api.github.com/users/rockt","html_url":"https://github.com/rockt","followers_url":"https://api.github.com/users/rockt/followers","following_url":"https://api.github.com/users/rockt/following{/other_user}","gists_url":"https://api.github.com/users/rockt/gists{/gist_id}","starred_url":"https://api.github.com/users/rockt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rockt/subscriptions","organizations_url":"https://api.github.com/users/rockt/orgs","repos_url":"https://api.github.com/users/rockt/repos","events_url":"https://api.github.com/users/rockt/events{/privacy}","received_events_url":"https://api.github.com/users/rockt/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2014-07-09T13:49:30Z","updated_at":"2016-11-04T10:44:59Z","closed_at":null,"body":"## Description:\n\nThe mutation \"p.F55>L\" is recognized by the SETHNER-component, but is uncorrectly tagged as INSDEL alltough it should be a SUBSTITION. The problem only occurs using the inexact grammar.\n\nIt seems the problem occurs in the **SETHNER.scala** line **274**\n lazy val ProteinIndel:P       = AALoc ~ (if(strictNomenclature)(\"delins\"|\"insdel\") else (\"delins\"|\"insdel\"|\">\") ^^ { InsDelString(_) }) ~ ((AA.+ ^^ { MutatedString(_) }) | Number)\nRemoving the \">\" fixes the problem, but the mutation is than no longer recognized\n## Minimal Java- example:\n\n```\n    SETHNER sethner = new SETHNER(false);\n    List<MutationMention> result = sethner.extractMutations(\"p.F55>L\");\n    for (MutationMention mutation : result) {\n        System.out.println(mutation);\n    }\n    System.out.println(\"Extracted \" + result.size() + \" mutations.\");\n```\n"},"comment":{"url":"https://api.github.com/repos/rockt/SETH/issues/comments/258398398","html_url":"https://github.com/rockt/SETH/issues/6#issuecomment-258398398","issue_url":"https://api.github.com/repos/rockt/SETH/issues/6","id":258398398,"user":{"login":"Erechtheus","id":3033565,"avatar_url":"https://avatars.githubusercontent.com/u/3033565?v=3","gravatar_id":"","url":"https://api.github.com/users/Erechtheus","html_url":"https://github.com/Erechtheus","followers_url":"https://api.github.com/users/Erechtheus/followers","following_url":"https://api.github.com/users/Erechtheus/following{/other_user}","gists_url":"https://api.github.com/users/Erechtheus/gists{/gist_id}","starred_url":"https://api.github.com/users/Erechtheus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Erechtheus/subscriptions","organizations_url":"https://api.github.com/users/Erechtheus/orgs","repos_url":"https://api.github.com/users/Erechtheus/repos","events_url":"https://api.github.com/users/Erechtheus/events{/privacy}","received_events_url":"https://api.github.com/users/Erechtheus/received_events","type":"User","site_admin":false},"created_at":"2016-11-04T10:44:59Z","updated_at":"2016-11-04T10:44:59Z","body":"Test code: https://github.com/rockt/SETH/blob/master/src/test/java/de/hu/berlin/wbi/issues/Issue6Test.java"}}
{"actor":{"display_login":"Erechtheus"}}