{"action":"created","issue":{"url":"https://api.github.com/repos/shaunpwilkinson/insect/issues/1","repository_url":"https://api.github.com/repos/shaunpwilkinson/insect","labels_url":"https://api.github.com/repos/shaunpwilkinson/insect/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/shaunpwilkinson/insect/issues/1/comments","events_url":"https://api.github.com/repos/shaunpwilkinson/insect/issues/1/events","html_url":"https://github.com/shaunpwilkinson/insect/issues/1","id":356450966,"node_id":"MDU6SXNzdWUzNTY0NTA5NjY=","number":1,"title":"Database request ITS2 fungi+plant","user":{"login":"andzandz11","id":19622117,"node_id":"MDQ6VXNlcjE5NjIyMTE3","avatar_url":"https://avatars3.githubusercontent.com/u/19622117?v=4","gravatar_id":"","url":"https://api.github.com/users/andzandz11","html_url":"https://github.com/andzandz11","followers_url":"https://api.github.com/users/andzandz11/followers","following_url":"https://api.github.com/users/andzandz11/following{/other_user}","gists_url":"https://api.github.com/users/andzandz11/gists{/gist_id}","starred_url":"https://api.github.com/users/andzandz11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andzandz11/subscriptions","organizations_url":"https://api.github.com/users/andzandz11/orgs","repos_url":"https://api.github.com/users/andzandz11/repos","events_url":"https://api.github.com/users/andzandz11/events{/privacy}","received_events_url":"https://api.github.com/users/andzandz11/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-09-03T10:38:18Z","updated_at":"2018-09-10T03:03:09Z","closed_at":null,"author_association":"NONE","body":"Can you maybe do a training for the ITS2 database that is commonly used by a lot of folks? It has ~370000 sequences and some working groups lack the computational resources. That would be great.\r\nI am trying to get things running to test the pipeline with my matK datbase, can make that available if it works.\r\n\r\nCould you please clarify how the learning step is done? Is something being alinged interally?\r\nI am a little bit concerned about the \"globally alignable\" criterion, because for ITS (in plants for example) that is not true. It has so many spontaneous (not dervied from an ancestor) indels that, if you zoom out far enough (to taxonomic level of order maybe) it violates the homology criterion very obviously, which is the basis of every alignment. It is alignable within one family (maybe even a few), but if you try to align ITS across the whole kingdom of plants the alignment gets >10000bp long and has >90% gaps. So is this package maybe not suitable for ITS (if it based on some kind of internal alignment)?  \r\n\r\nThanks!\r\n\r\n\r\nPS: I see you also noticed some GenBank queries give unreproduceable errors. I usually spilt my query (using R package rentrez functions) up to a lot of fast queries (like 2000 sequeces per query) and wrap it up like this:\r\nThere is probably a better way to do this, but it works. If you download hundreds of thousands of sequences on a weekly basis this is really a life saver.\r\n\r\n```\r\nrepeat_on_fail <- function(fun, max_attempt = 3, ...)\r\n{\r\n  r <- NULL\r\n  attempt <- 1\r\n  while( is.null(r) && attempt <= max_attempt ) \r\n   {\r\n    attempt <- attempt + 1\r\n    try( r <- fun(...) )\r\n   }\r\n  r\r\n}\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/shaunpwilkinson/insect/issues/comments/419774180","html_url":"https://github.com/shaunpwilkinson/insect/issues/1#issuecomment-419774180","issue_url":"https://api.github.com/repos/shaunpwilkinson/insect/issues/1","id":419774180,"node_id":"MDEyOklzc3VlQ29tbWVudDQxOTc3NDE4MA==","user":{"login":"shaunpwilkinson","id":10361217,"node_id":"MDQ6VXNlcjEwMzYxMjE3","avatar_url":"https://avatars0.githubusercontent.com/u/10361217?v=4","gravatar_id":"","url":"https://api.github.com/users/shaunpwilkinson","html_url":"https://github.com/shaunpwilkinson","followers_url":"https://api.github.com/users/shaunpwilkinson/followers","following_url":"https://api.github.com/users/shaunpwilkinson/following{/other_user}","gists_url":"https://api.github.com/users/shaunpwilkinson/gists{/gist_id}","starred_url":"https://api.github.com/users/shaunpwilkinson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shaunpwilkinson/subscriptions","organizations_url":"https://api.github.com/users/shaunpwilkinson/orgs","repos_url":"https://api.github.com/users/shaunpwilkinson/repos","events_url":"https://api.github.com/users/shaunpwilkinson/events{/privacy}","received_events_url":"https://api.github.com/users/shaunpwilkinson/received_events","type":"User","site_admin":false},"created_at":"2018-09-10T03:03:09Z","updated_at":"2018-09-10T03:03:09Z","author_association":"OWNER","body":"I usually leave the conserved ends on since they often play an important role in the first few recursive decisions before the noisy non-coding region kicks in towards the tips of the classification tree. I find having both the fast- and slow-evolving regions generally gives better discriminatory power overall. One option is to just include a handful of residues either side of the spacer, in order to capture as many training sequences as possible (i.e. sequences generated with a wide range of different primer sets). I'll make it a priority to generate a plant ITS2 classifier as soon as I get a chance. Thanks for those links too, will check them out.    "}}
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