{"action":"created","issue":{"url":"https://api.github.com/repos/jhcepas/ete/issues/137","labels_url":"https://api.github.com/repos/jhcepas/ete/issues/137/labels{/name}","comments_url":"https://api.github.com/repos/jhcepas/ete/issues/137/comments","events_url":"https://api.github.com/repos/jhcepas/ete/issues/137/events","html_url":"https://github.com/jhcepas/ete/issues/137","id":107905949,"number":137,"title":"interoperability with scikit-bio","user":{"login":"jhcepas","id":163658,"avatar_url":"https://avatars.githubusercontent.com/u/163658?v=3","gravatar_id":"","url":"https://api.github.com/users/jhcepas","html_url":"https://github.com/jhcepas","followers_url":"https://api.github.com/users/jhcepas/followers","following_url":"https://api.github.com/users/jhcepas/following{/other_user}","gists_url":"https://api.github.com/users/jhcepas/gists{/gist_id}","starred_url":"https://api.github.com/users/jhcepas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhcepas/subscriptions","organizations_url":"https://api.github.com/users/jhcepas/orgs","repos_url":"https://api.github.com/users/jhcepas/repos","events_url":"https://api.github.com/users/jhcepas/events{/privacy}","received_events_url":"https://api.github.com/users/jhcepas/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/jhcepas/ete/labels/feature%20request","name":"feature request","color":"d4c5f9"}],"state":"open","locked":false,"assignee":{"login":"jhcepas","id":163658,"avatar_url":"https://avatars.githubusercontent.com/u/163658?v=3","gravatar_id":"","url":"https://api.github.com/users/jhcepas","html_url":"https://github.com/jhcepas","followers_url":"https://api.github.com/users/jhcepas/followers","following_url":"https://api.github.com/users/jhcepas/following{/other_user}","gists_url":"https://api.github.com/users/jhcepas/gists{/gist_id}","starred_url":"https://api.github.com/users/jhcepas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhcepas/subscriptions","organizations_url":"https://api.github.com/users/jhcepas/orgs","repos_url":"https://api.github.com/users/jhcepas/repos","events_url":"https://api.github.com/users/jhcepas/events{/privacy}","received_events_url":"https://api.github.com/users/jhcepas/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/jhcepas/ete/milestones/5","html_url":"https://github.com/jhcepas/ete/milestones/3.0","labels_url":"https://api.github.com/repos/jhcepas/ete/milestones/5/labels","id":3176,"number":5,"title":"3.0","description":"","creator":{"login":"jhcepas","id":163658,"avatar_url":"https://avatars.githubusercontent.com/u/163658?v=3","gravatar_id":"","url":"https://api.github.com/users/jhcepas","html_url":"https://github.com/jhcepas","followers_url":"https://api.github.com/users/jhcepas/followers","following_url":"https://api.github.com/users/jhcepas/following{/other_user}","gists_url":"https://api.github.com/users/jhcepas/gists{/gist_id}","starred_url":"https://api.github.com/users/jhcepas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhcepas/subscriptions","organizations_url":"https://api.github.com/users/jhcepas/orgs","repos_url":"https://api.github.com/users/jhcepas/repos","events_url":"https://api.github.com/users/jhcepas/events{/privacy}","received_events_url":"https://api.github.com/users/jhcepas/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":1,"state":"open","created_at":"2011-04-14T20:20:33Z","updated_at":"2015-11-18T11:01:22Z","due_on":null,"closed_at":null},"comments":10,"created_at":"2015-09-23T12:08:07Z","updated_at":"2015-11-25T18:07:20Z","closed_at":null,"body":"something like `Tree.from_skbio(...)` and `Tree.as_skbio(...)` \r\n\r\n1) The method should accept/return skbio Tree instances.\r\n2) Is it possible to avoid newick serialisation? \r\n3) any special attributes in skbio Trees that need to be converted?\r\n4) support for alignment objects?\r\n5) any idea or feature request for a better integration between packages?\r\n\r\nAn alternative would be to overload the constructor and support the following syntax by detecting the input instance type:\r\n`tree = eteTree(skbioTree, alignment=skbioAlg)`\r\nI personally find this approach more natural. Any potential problem?\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/jhcepas/ete/issues/comments/159690195","html_url":"https://github.com/jhcepas/ete/issues/137#issuecomment-159690195","issue_url":"https://api.github.com/repos/jhcepas/ete/issues/137","id":159690195,"user":{"login":"wasade","id":474290,"avatar_url":"https://avatars.githubusercontent.com/u/474290?v=3","gravatar_id":"","url":"https://api.github.com/users/wasade","html_url":"https://github.com/wasade","followers_url":"https://api.github.com/users/wasade/followers","following_url":"https://api.github.com/users/wasade/following{/other_user}","gists_url":"https://api.github.com/users/wasade/gists{/gist_id}","starred_url":"https://api.github.com/users/wasade/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wasade/subscriptions","organizations_url":"https://api.github.com/users/wasade/orgs","repos_url":"https://api.github.com/users/wasade/repos","events_url":"https://api.github.com/users/wasade/events{/privacy}","received_events_url":"https://api.github.com/users/wasade/received_events","type":"User","site_admin":false},"created_at":"2015-11-25T18:07:20Z","updated_at":"2015-11-25T18:07:20Z","body":"The path of least resistance might be to assign unique node names, and\nserialize a dict of attributes keyed by the node name? The more\ncomprehensive solution may be to write an extended newick parser for skbio\n\nOn Wed, Nov 25, 2015 at 9:48 AM, Jaime Huerta-Cepas <\nnotifications@github.com> wrote:\n\n> ok, I wil stick to 1\n> ete stores node features as normal attributes, but keeps track of them to\n> know what to export in extended newick format some other minor things.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/jhcepas/ete/issues/137#issuecomment-159685985>.\n>\n"}}