{"action":"opened","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/28","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/28/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/28/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/28/events","html_url":"https://github.com/cjfields/redmine-test/issues/28","id":95351110,"number":28,"title":"informative codons method for kaks -- Bio/Align/DNAStatistics.pm","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Category:%20Core%20Components","name":"Category: Core Components","color":"006699"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Component:%20URL","name":"Component: URL","color":"ededed"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Low","name":"Priority: Low","color":"009933"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Feature","name":"Tracker: Feature","color":"FF6600"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1","html_url":"https://github.com/cjfields/redmine-test/milestones/main-trunk","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1/labels","id":1210607,"number":1,"title":"main-trunk","description":null,"creator":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"open_issues":12,"closed_issues":0,"state":"open","created_at":"2015-07-16T04:51:18Z","updated_at":"2015-07-16T05:04:20Z","due_on":null,"closed_at":null},"comments":0,"created_at":"2015-07-16T05:04:20Z","updated_at":"2015-07-16T05:04:20Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Albert Vilella** (Albert Vilella)\nOriginal Redmine Issue: 2078, https://redmine.open-bio.org/issues/2078\nOriginal Date: 2006-08-17\nOriginal Assignee: Bioperl Guts\n\n---\n\nI think it would be nice to have a method in\nBio/Align/DNAStatistics.pm that gives the number of informative codons\nfor kaks in a MSA. That is, the codons that are used in the\ncalculation of kaks. This, AFAIK, more or less what codeml calls\n“patterns”.\n\nI often find myself in the situation of wanting to know how big is the\nCDS alignment not in terms of sequence length, but of the number of\ncodons that are going to be used in the kaks statistics. I guess this\nmethod would help in that.\n\nThe method could:\n\nreturn the number of informative codons?\nmaybe return a new seqarray with only the informative codons?\n\nWhat you reckon? Jason? Chris?\n\n\n\n\n"}}