{"action":"created","issue":{"url":"https://api.github.com/repos/OpenTreeOfLife/otcetera/issues/3","labels_url":"https://api.github.com/repos/OpenTreeOfLife/otcetera/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/OpenTreeOfLife/otcetera/issues/3/comments","events_url":"https://api.github.com/repos/OpenTreeOfLife/otcetera/issues/3/events","html_url":"https://github.com/OpenTreeOfLife/otcetera/issues/3","id":65015105,"number":3,"title":"otcprunetaxonomy not working correctly(?)","user":{"login":"josephwb","id":808499,"avatar_url":"https://avatars.githubusercontent.com/u/808499?v=3","gravatar_id":"","url":"https://api.github.com/users/josephwb","html_url":"https://github.com/josephwb","followers_url":"https://api.github.com/users/josephwb/followers","following_url":"https://api.github.com/users/josephwb/following{/other_user}","gists_url":"https://api.github.com/users/josephwb/gists{/gist_id}","starred_url":"https://api.github.com/users/josephwb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josephwb/subscriptions","organizations_url":"https://api.github.com/users/josephwb/orgs","repos_url":"https://api.github.com/users/josephwb/repos","events_url":"https://api.github.com/users/josephwb/events{/privacy}","received_events_url":"https://api.github.com/users/josephwb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-03-29T02:51:36Z","updated_at":"2015-03-30T12:14:39Z","closed_at":null,"body":"I'm trying to test sub-synth trees for unsupported edges, but am having problems with \"missing\" OTT IDs (specifically, an OTT ID present in the taxonomy, but not the synth tree or input trees).\r\n\r\nWhat I am doing:\r\nFirst: prune the taxonomy tree using the synthetic tree label set:\r\n```bash\r\njosephwb@WOPR:~/Desktop/test_synth$ otcprunetaxonomy Fungi_taxonomy.tre fungi.synth.tre > Pruned_Fungi_taxonomy.tre\r\n2015-03-28 22:37:40,470 INFO  [default] reading \"Fungi_taxonomy.tre\"...\r\n2015-03-28 22:37:46,285 INFO  [default] reading \"fungi.synth.tre\"...\r\n```\r\nSecond: run the unsupported edge test:\r\n```bash\r\njosephwb@WOPR:~/Desktop/test_synth$ otcfindunsupportednodes Pruned_Fungi_taxonomy.tre fungi.synth.tre fungitrees/*.tre\r\n2015-03-28 22:38:32,261 INFO  [default] reading \"Pruned_Fungi_taxonomy.tre\"...\r\n2015-03-28 22:38:41,683 INFO  [default] reading \"fungi.synth.tre\"...\r\n2015-03-28 22:38:49,124 INFO  [default] reading \"fungitrees/ott1010493.tre\"...\r\n2015-03-28 22:38:49,124 INFO  [default] reading \"fungitrees/ott1026597.tre\"...\r\n2015-03-28 22:38:49,126 INFO  [default] reading \"fungitrees/ott103001.tre\"...\r\n2015-03-28 22:38:49,127 INFO  [default] reading \"fungitrees/ott103002.tre\"...\r\n2015-03-28 22:38:49,132 INFO  [default] reading \"fungitrees/ott1031212.tre\"...\r\n2015-03-28 22:38:49,132 INFO  [default] reading \"fungitrees/ott104185.tre\"...\r\n2015-03-28 22:38:51,161 INFO  [default] reading \"fungitrees/ott1082072.tre\"...\r\n2015-03-28 22:38:51,166 INFO  [default] reading \"fungitrees/ott1098854.tre\"...\r\nERROR. Exiting due to an exception:\r\nOTT id not found 4085684\r\n```\r\nThe OTT ID 4085684 appears both in my original \"Fungi_taxonomy.tre\" and otcetera-generated \"Pruned_Fungi_taxonomy.tre\". The taxon itself is barren. I can filter such \"dubious\" taxa from my taxonomy tree, but I thought ```otcprunetaxonomy``` would accomplish this."},"comment":{"url":"https://api.github.com/repos/OpenTreeOfLife/otcetera/issues/comments/87653347","html_url":"https://github.com/OpenTreeOfLife/otcetera/issues/3#issuecomment-87653347","issue_url":"https://api.github.com/repos/OpenTreeOfLife/otcetera/issues/3","id":87653347,"user":{"login":"josephwb","id":808499,"avatar_url":"https://avatars.githubusercontent.com/u/808499?v=3","gravatar_id":"","url":"https://api.github.com/users/josephwb","html_url":"https://github.com/josephwb","followers_url":"https://api.github.com/users/josephwb/followers","following_url":"https://api.github.com/users/josephwb/following{/other_user}","gists_url":"https://api.github.com/users/josephwb/gists{/gist_id}","starred_url":"https://api.github.com/users/josephwb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josephwb/subscriptions","organizations_url":"https://api.github.com/users/josephwb/orgs","repos_url":"https://api.github.com/users/josephwb/repos","events_url":"https://api.github.com/users/josephwb/events{/privacy}","received_events_url":"https://api.github.com/users/josephwb/received_events","type":"User","site_admin":false},"created_at":"2015-03-30T12:14:39Z","updated_at":"2015-03-30T12:14:39Z","body":"Ok, yeah, I just included the wrong files in the link above. [This one](https://www.dropbox.com/s/ezwlui9xeiee7js/for_MTH2.tgz?dl=0) should work (or, er, shouldn't work. As expected, that is.).\r\n\r\n```\r\ngrep 4085684 Unfiltered_Fungi_taxonomy.tre\r\n# TRUE\r\ngrep 4085684 fungi.synth.tre\r\n# FALSE\r\notcprunetaxonomy Unfiltered_Fungi_taxonomy.tre fungi.synth.tre > Pruned_Fungi_taxonomy.tre\r\ngrep 4085684 Pruned_Fungi_taxonomy.tre\r\n# TRUE\r\n```"}}