{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/1175","labels_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1175/labels{/name}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1175/comments","events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1175/events","html_url":"https://github.com/biocore/scikit-bio/issues/1175","id":115349110,"number":1175,"title":"support custom grammared sequence types","user":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/biocore/scikit-bio/labels/API","name":"API","color":"c7def8"},{"url":"https://api.github.com/repos/biocore/scikit-bio/labels/enhancement","name":"enhancement","color":"006b75"}],"state":"open","locked":false,"assignee":{"login":"anderspitman","id":7820200,"avatar_url":"https://avatars.githubusercontent.com/u/7820200?v=3","gravatar_id":"","url":"https://api.github.com/users/anderspitman","html_url":"https://github.com/anderspitman","followers_url":"https://api.github.com/users/anderspitman/followers","following_url":"https://api.github.com/users/anderspitman/following{/other_user}","gists_url":"https://api.github.com/users/anderspitman/gists{/gist_id}","starred_url":"https://api.github.com/users/anderspitman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anderspitman/subscriptions","organizations_url":"https://api.github.com/users/anderspitman/orgs","repos_url":"https://api.github.com/users/anderspitman/repos","events_url":"https://api.github.com/users/anderspitman/events{/privacy}","received_events_url":"https://api.github.com/users/anderspitman/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/biocore/scikit-bio/milestones/14","html_url":"https://github.com/biocore/scikit-bio/milestones/0.4.1","labels_url":"https://api.github.com/repos/biocore/scikit-bio/milestones/14/labels","id":1389454,"number":14,"title":"0.4.1","description":"This release will have Python 2 and Python 3 support. ","creator":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":26,"state":"open","created_at":"2015-11-02T17:11:28Z","updated_at":"2015-12-09T23:44:23Z","due_on":"2015-12-09T07:00:00Z","closed_at":null},"comments":29,"created_at":"2015-11-05T18:55:31Z","updated_at":"2015-12-09T23:53:51Z","closed_at":null,"body":"Changes:\r\n\r\n- [ ] rename  `skbio.sequence._iupac_sequence.IUPACSequence` class to `GrammaredSequence`: it is a sequence that conforms to the scikit-bio sequence grammar (based on IUPAC's notion of degenerates, gaps, nondegenerates, etc. but not necessarily constrained to the IUPAC alphabet).\r\n\r\n- [ ] make `GrammaredSequence` publicly importable from `skbio.sequence`\r\n\r\n- [ ] document `GrammaredSequence` as a place for users to inherit from to create grammared sequences with custom alphabets (add a doctest example of this too).\r\n\r\n- [ ] for `GrammaredSequence` make a metaclass that performs validation of its alphabet (e.g., `default_gap_char` should be present in `gap_chars`; degenerates must expand into valid nondegenerates; etc.)\r\n\r\n- [ ] make it impossible to inherit from DNA, RNA, and Protein and document why"},"comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments/163440448","html_url":"https://github.com/biocore/scikit-bio/issues/1175#issuecomment-163440448","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1175","id":163440448,"user":{"login":"ebolyen","id":3976804,"avatar_url":"https://avatars.githubusercontent.com/u/3976804?v=3","gravatar_id":"","url":"https://api.github.com/users/ebolyen","html_url":"https://github.com/ebolyen","followers_url":"https://api.github.com/users/ebolyen/followers","following_url":"https://api.github.com/users/ebolyen/following{/other_user}","gists_url":"https://api.github.com/users/ebolyen/gists{/gist_id}","starred_url":"https://api.github.com/users/ebolyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ebolyen/subscriptions","organizations_url":"https://api.github.com/users/ebolyen/orgs","repos_url":"https://api.github.com/users/ebolyen/repos","events_url":"https://api.github.com/users/ebolyen/events{/privacy}","received_events_url":"https://api.github.com/users/ebolyen/received_events","type":"User","site_admin":false},"created_at":"2015-12-09T23:53:51Z","updated_at":"2015-12-09T23:53:51Z","body":"@anderspitman We're going to bump this to the next release, so there's a ton of time to figure this out now."}}