{"action":"created","issue":{"url":"https://api.github.com/repos/rdpstaff/classifier/issues/18","repository_url":"https://api.github.com/repos/rdpstaff/classifier","labels_url":"https://api.github.com/repos/rdpstaff/classifier/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/rdpstaff/classifier/issues/18/comments","events_url":"https://api.github.com/repos/rdpstaff/classifier/issues/18/events","html_url":"https://github.com/rdpstaff/classifier/issues/18","id":192645576,"number":18,"title":"How to format the taxonomy file to retrain classifier","user":{"login":"yingeddi2008","id":7376851,"avatar_url":"https://avatars.githubusercontent.com/u/7376851?v=3","gravatar_id":"","url":"https://api.github.com/users/yingeddi2008","html_url":"https://github.com/yingeddi2008","followers_url":"https://api.github.com/users/yingeddi2008/followers","following_url":"https://api.github.com/users/yingeddi2008/following{/other_user}","gists_url":"https://api.github.com/users/yingeddi2008/gists{/gist_id}","starred_url":"https://api.github.com/users/yingeddi2008/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yingeddi2008/subscriptions","organizations_url":"https://api.github.com/users/yingeddi2008/orgs","repos_url":"https://api.github.com/users/yingeddi2008/repos","events_url":"https://api.github.com/users/yingeddi2008/events{/privacy}","received_events_url":"https://api.github.com/users/yingeddi2008/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-11-30T18:41:58Z","updated_at":"2016-12-01T18:55:21Z","closed_at":null,"body":"Hi rdp staff,\r\n\r\nI am trying to retrain RDP classifier using NCBI 16s database, however, when I looked into the example taxonomy file and the fasta file, I am a bit confused how should I even generate that file.\r\n```\r\n0*Root*-1*0*rootrank\r\n1*Bacteria*0*1*domain\r\n2*\"Actinobacteria\"*1*2*phylum\r\n3*Actinobacteria*2*3*class\r\n4*Acidimicrobidae*3*4*subclass\r\n5*Acidimicrobiales*4*5*order\r\n6*\"Acidimicrobineae\"*5*6*suborder\r\n7*Acidimicrobiaceae*6*7*family\r\n8*Acidimicrobium*7*8*genus\r\n9*Ferrimicrobium*7*8*genus\r\n10*Ferrithrix*7*8*genus\r\n11*Ilumatobacter*7*8*genus\r\n12*Iamiaceae*6*7*family\r\n3102*Aquihabitans*12*8*genus\r\n13*Iamia*12*8*genus\r\n```\r\n\r\nCould you please explain how each line is constructed? Allow me to take a line as an example, \r\n```\r\n6*\"Acidimicrobineae\"*5*6*suborder\r\n```\r\nI could guess that the first number is the taxonomy id for **Acidimicrobineae**, which is 6, and its parent taxonomy is 5, Acidimicrobiales. I assume that the _suborder_ at the end of the line indicates that **Acidimicrobineae** is at the taxonomy rank of suborder, right? Then what is the 6 before _suborder_ mean?  when I look at ``` 12*Iamiaceae*6*7*family```, I can say Iamiaceae is a family level taxonomy, which has the parent of 6  (Acidimicrobineae) and 7 (Acidimicrobiaceae)? I am not sure I am getting what's the rule of constructing the taxonomy file here. Could you please explain how this is done?\r\n\r\nThanks in advance,\r\n\r\nEddi"},"comment":{"url":"https://api.github.com/repos/rdpstaff/classifier/issues/comments/264260128","html_url":"https://github.com/rdpstaff/classifier/issues/18#issuecomment-264260128","issue_url":"https://api.github.com/repos/rdpstaff/classifier/issues/18","id":264260128,"user":{"login":"yingeddi2008","id":7376851,"avatar_url":"https://avatars.githubusercontent.com/u/7376851?v=3","gravatar_id":"","url":"https://api.github.com/users/yingeddi2008","html_url":"https://github.com/yingeddi2008","followers_url":"https://api.github.com/users/yingeddi2008/followers","following_url":"https://api.github.com/users/yingeddi2008/following{/other_user}","gists_url":"https://api.github.com/users/yingeddi2008/gists{/gist_id}","starred_url":"https://api.github.com/users/yingeddi2008/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yingeddi2008/subscriptions","organizations_url":"https://api.github.com/users/yingeddi2008/orgs","repos_url":"https://api.github.com/users/yingeddi2008/repos","events_url":"https://api.github.com/users/yingeddi2008/events{/privacy}","received_events_url":"https://api.github.com/users/yingeddi2008/received_events","type":"User","site_admin":false},"created_at":"2016-12-01T18:55:21Z","updated_at":"2016-12-01T18:55:21Z","body":"You can send the scripts to hlin2@luc.edu. Thanks."}}
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