{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1844","repository_url":"https://api.github.com/repos/OpenMS/OpenMS","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1844/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1844/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1844/events","html_url":"https://github.com/OpenMS/OpenMS/pull/1844","id":136464685,"number":1844,"title":"Feature luciphor2","user":{"login":"PetraGutenbrunner","id":6952271,"avatar_url":"https://avatars.githubusercontent.com/u/6952271?v=3","gravatar_id":"","url":"https://api.github.com/users/PetraGutenbrunner","html_url":"https://github.com/PetraGutenbrunner","followers_url":"https://api.github.com/users/PetraGutenbrunner/followers","following_url":"https://api.github.com/users/PetraGutenbrunner/following{/other_user}","gists_url":"https://api.github.com/users/PetraGutenbrunner/gists{/gist_id}","starred_url":"https://api.github.com/users/PetraGutenbrunner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PetraGutenbrunner/subscriptions","organizations_url":"https://api.github.com/users/PetraGutenbrunner/orgs","repos_url":"https://api.github.com/users/PetraGutenbrunner/repos","events_url":"https://api.github.com/users/PetraGutenbrunner/events{/privacy}","received_events_url":"https://api.github.com/users/PetraGutenbrunner/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-02-25T18:05:43Z","updated_at":"2016-02-27T21:12:13Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1844","html_url":"https://github.com/OpenMS/OpenMS/pull/1844","diff_url":"https://github.com/OpenMS/OpenMS/pull/1844.diff","patch_url":"https://github.com/OpenMS/OpenMS/pull/1844.patch"},"body":"In addition to the algorithm Ascore (PhosphoScoring) LuciPHOr2 is an algorithm for site localisation of generic post-translational modifications from tandem mass spectrometry data with false localisation rate using modified target-decoy approach (DOI: 10.1093/bioinformatics/btu788)\r\nLuciphorAdapter is a wrapper around that luciphor2.jar file.\r\n\r\nChanges:\r\n* PepXML: set score values for percolator, and treat percolator analysis like a peptide prophet analysis. This is necessary because the input for luciphor is a pepXML and therfore all score informations must be available.\r\n* PepXML: add spectrum information to file because Luciphor needs the spectrum index as spectrum lookup\r\n* ConsensusID: copy search parameters to new output file. This is necessary, because the modification search parameters are needed to convert the luciphor sequence format to the OpenMS format. Modifications are in Luciphor lowercase (E.g. VLLRsL -> VLLRS(Phospho))\r\n\r\nFor more details please look up the commit messages.\r\n"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/189726716","html_url":"https://github.com/OpenMS/OpenMS/pull/1844#issuecomment-189726716","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1844","id":189726716,"user":{"login":"timosachsenberg","id":5803621,"avatar_url":"https://avatars.githubusercontent.com/u/5803621?v=3","gravatar_id":"","url":"https://api.github.com/users/timosachsenberg","html_url":"https://github.com/timosachsenberg","followers_url":"https://api.github.com/users/timosachsenberg/followers","following_url":"https://api.github.com/users/timosachsenberg/following{/other_user}","gists_url":"https://api.github.com/users/timosachsenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/timosachsenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timosachsenberg/subscriptions","organizations_url":"https://api.github.com/users/timosachsenberg/orgs","repos_url":"https://api.github.com/users/timosachsenberg/repos","events_url":"https://api.github.com/users/timosachsenberg/events{/privacy}","received_events_url":"https://api.github.com/users/timosachsenberg/received_events","type":"User","site_admin":false},"created_at":"2016-02-27T21:12:13Z","updated_at":"2016-02-27T21:12:13Z","body":"Nice addition. Could you check if the parameter names for tolerance and unit is the same as on other tools? Could you also add a note which version it has been developed for. By the way - what is the license of luciphor? Maybe we can package it."}}