{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/453","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/453/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/453/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/453/events","html_url":"https://github.com/GMOD/Apollo/issues/453","id":90744798,"number":453,"title":"Peptide sequence export rules","user":{"login":"cmdcolin","id":6511937,"avatar_url":"https://avatars.githubusercontent.com/u/6511937?v=3","gravatar_id":"","url":"https://api.github.com/users/cmdcolin","html_url":"https://github.com/cmdcolin","followers_url":"https://api.github.com/users/cmdcolin/followers","following_url":"https://api.github.com/users/cmdcolin/following{/other_user}","gists_url":"https://api.github.com/users/cmdcolin/gists{/gist_id}","starred_url":"https://api.github.com/users/cmdcolin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmdcolin/subscriptions","organizations_url":"https://api.github.com/users/cmdcolin/orgs","repos_url":"https://api.github.com/users/cmdcolin/repos","events_url":"https://api.github.com/users/cmdcolin/events{/privacy}","received_events_url":"https://api.github.com/users/cmdcolin/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/GMOD/Apollo/labels/discussion","name":"discussion","color":"cc317c"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/Important","name":"Important","color":"eb6420"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/Review","name":"Review","color":"fef2c0"}],"state":"open","locked":false,"assignee":{"login":"deepakunni3","id":4530272,"avatar_url":"https://avatars.githubusercontent.com/u/4530272?v=3","gravatar_id":"","url":"https://api.github.com/users/deepakunni3","html_url":"https://github.com/deepakunni3","followers_url":"https://api.github.com/users/deepakunni3/followers","following_url":"https://api.github.com/users/deepakunni3/following{/other_user}","gists_url":"https://api.github.com/users/deepakunni3/gists{/gist_id}","starred_url":"https://api.github.com/users/deepakunni3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deepakunni3/subscriptions","organizations_url":"https://api.github.com/users/deepakunni3/orgs","repos_url":"https://api.github.com/users/deepakunni3/repos","events_url":"https://api.github.com/users/deepakunni3/events{/privacy}","received_events_url":"https://api.github.com/users/deepakunni3/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/GMOD/Apollo/milestones/15","html_url":"https://github.com/GMOD/Apollo/milestones/2.0.0-RC2","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/15/labels","id":1185971,"number":15,"title":"2.0.0-RC2","description":"","creator":{"login":"cmdcolin","id":6511937,"avatar_url":"https://avatars.githubusercontent.com/u/6511937?v=3","gravatar_id":"","url":"https://api.github.com/users/cmdcolin","html_url":"https://github.com/cmdcolin","followers_url":"https://api.github.com/users/cmdcolin/followers","following_url":"https://api.github.com/users/cmdcolin/following{/other_user}","gists_url":"https://api.github.com/users/cmdcolin/gists{/gist_id}","starred_url":"https://api.github.com/users/cmdcolin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmdcolin/subscriptions","organizations_url":"https://api.github.com/users/cmdcolin/orgs","repos_url":"https://api.github.com/users/cmdcolin/repos","events_url":"https://api.github.com/users/cmdcolin/events{/privacy}","received_events_url":"https://api.github.com/users/cmdcolin/received_events","type":"User","site_admin":false},"open_issues":17,"closed_issues":5,"state":"open","created_at":"2015-06-29T19:41:50Z","updated_at":"2015-07-09T16:31:02Z","due_on":"2015-07-10T05:00:00Z","closed_at":null},"comments":11,"created_at":"2015-06-24T17:57:10Z","updated_at":"2015-07-09T21:22:38Z","closed_at":null,"body":"From the #448 issue about stop codons, we had a discussion about peptide sequence exports.\r\n\r\n\r\nIn that thread, we had an annotation that looks like this:\r\n\r\n![1234](https://cloud.githubusercontent.com/assets/6511937/8337006/ec93b646-1a6d-11e5-8bcf-23f3785a2626.png)\r\n\r\nThis has an in frame stop codon\r\n\r\n![4567](https://cloud.githubusercontent.com/assets/6511937/8337342/40b7b252-1a70-11e5-854c-008cba3dfa51.png)\r\n\r\nThis essentially shows how our annotation essentially \"trusts\" the evidence track, and does not try to calculate longest ORF on import.\r\n\r\nYet, our exported peptide is still trying to \"follow\" the stop codons in the sequence, so the sequence that we get is highly truncated in this case.\r\n\r\nIn our old official gene sets, we would ignore these stop codons and place X's instead.\r\n\r\nFor example, it would be\r\n\r\n    >gnl|Sinv_1.0|SINV10883-PA\r\n    LVSMSMEYLVLRLRPLAGIRRAPDNLRRXLRRETQLRPFYAXHRVASRHVASRRASRHVS\r\n    SRHFTSRHITATK(X)EDSTRRSVIECRSVDLGRRAILAKICWNFRLGIRVRKSHPVTPLRR\r\n    HETVDRRPRRYVSRVLDVQVNVLLRLTEEVVYLLHGAERTDLLLGAVGDEPPGGAGRSSA\r\n    VINDVRVTVGIDXARSRSRRSXQPPAIAERNRGFGASVSHRLXLRVFKVYIGIALGVNRE\r\n    SPATFLSDCEPRHRRRRRRRRHRRRPRVGARRRCPSGGGAQSGSVSRSDGDTGITGSRGD\r\n    SHIGRIAVGSQADIEVPTCLRKFPAGKDGRGWRWGXGRSLACNQGVLCSQQQVAVSQKRT\r\n    VRARRAARSESSGGRLGGGGDRQGHPLRFSXKGARRPIAAQDRPRRLVLDAXDRPRVAIV\r\n    EIVXMMRLRRSLFPACR\r\n\r\n\r\nIn our current case (WA1.0, WA2.0 still needs to address #448), we are stopping at the first stop codon though.\r\n\r\n    >SINV10883-RA\r\n    LVSMSMEYLVLRLRPLAGIRRAPDNLRRLRRETQLRPFYAHRVASRHVASRRASRHVS\r\n    SRHFTSRHITATK\r\n\r\n\r\n\r\n@deepakunni3 outlined a case for modified export rules that I thought were compelling:\r\n\r\n1) on import, annotation CDS boundaries are trusted (currently doing this)\r\n2) if a exon boundary is changed, then setLongestORF is called so CDS boundaries are recalculated (currently doing this)\r\n3) therefore, if the exon boundaries are unchanged, then we can trust the CDS boundaries, and export the peptides for that whole CDS even if there are stops in it. (not doing this, we attempt to truncate protein sequence despite CDS being longer)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/120147795","html_url":"https://github.com/GMOD/Apollo/issues/453#issuecomment-120147795","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/453","id":120147795,"user":{"login":"deepakunni3","id":4530272,"avatar_url":"https://avatars.githubusercontent.com/u/4530272?v=3","gravatar_id":"","url":"https://api.github.com/users/deepakunni3","html_url":"https://github.com/deepakunni3","followers_url":"https://api.github.com/users/deepakunni3/followers","following_url":"https://api.github.com/users/deepakunni3/following{/other_user}","gists_url":"https://api.github.com/users/deepakunni3/gists{/gist_id}","starred_url":"https://api.github.com/users/deepakunni3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deepakunni3/subscriptions","organizations_url":"https://api.github.com/users/deepakunni3/orgs","repos_url":"https://api.github.com/users/deepakunni3/repos","events_url":"https://api.github.com/users/deepakunni3/events{/privacy}","received_events_url":"https://api.github.com/users/deepakunni3/received_events","type":"User","site_admin":false},"created_at":"2015-07-09T21:22:38Z","updated_at":"2015-07-09T21:22:38Z","body":"Commit 6419e12 (on issue456 branch) fixes this bug. "}}