{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/1813","labels_url":"https://api.github.com/repos/biocore/qiime/issues/1813/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/1813/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/1813/events","html_url":"https://github.com/biocore/qiime/issues/1813","id":52782270,"number":1813,"title":"differential_abundance.py bug/doc fixes","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":[],"state":"closed","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/biocore/qiime/milestones/21","labels_url":"https://api.github.com/repos/biocore/qiime/milestones/21/labels","id":530599,"number":21,"title":"QIIME 1.9.0","description":"This will likely be the last minor release under QIIME 1. ","creator":{"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},"open_issues":19,"closed_issues":240,"state":"open","created_at":"2014-01-08T19:45:01Z","updated_at":"2015-01-08T18:02:44Z","due_on":"2014-12-19T07:00:00Z","closed_at":null},"comments":1,"created_at":"2014-12-23T23:03:42Z","updated_at":"2015-01-08T18:02:44Z","closed_at":"2015-01-08T18:02:44Z","body":"The following changes need to be made to differential_abundance.py prior to the 1.9.0 release:\r\n\r\n- [x] when passing a category via `-c` that isn't in the mapping file, an uninformative error message is produced:\r\n\r\n```\r\ndifferential_abundance.py -i otu_table.biom -o DE_OTUs.txt -m map.txt -a metagenomeSeq_fitZIG -c not-real -x Control -y Fast\r\nTraceback (most recent call last):\r\n File \"/Users/caporaso/.virtualenvs/qiime/bin/differential_abundance.py\", line 10, in <module>\r\n   execfile(__file__)\r\n File \"/Users/caporaso/Dropbox/code/Qiime/scripts/differential_abundance.py\", line 88, in <module>\r\n   main()\r\n File \"/Users/caporaso/Dropbox/code/Qiime/scripts/differential_abundance.py\", line 73, in main\r\n   DA_fitZIG(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2)\r\n File \"/Users/caporaso/Dropbox/code/Qiime/qiime/differential_abundance.py\", line 32, in DA_fitZIG\r\n   run_fitZIG(json_infile, out_path, mapping_category, subcategory_1, subcategory_2)\r\n File \"/Users/caporaso/Dropbox/code/Qiime/qiime/differential_abundance.py\", line 69, in run_fitZIG\r\n   app_result = rsl(command_args=command_args, script_name='fitZIG.r')\r\n File \"/Users/caporaso/Dropbox/code/Qiime/qiime/util.py\", line 2006, in __call__\r\n   % (''.join(open(errfilepath, 'r').readlines())))\r\nburrito.util.ApplicationError: Unacceptable application exit status: 1, command: cd \"/Users/caporaso/Dropbox/code/Qiime/qiime_test_data/differential_abundance/\";  R --slave --args --source_dir /Users/caporaso/Dropbox/code/Qiime/qiime/support_files/R -i otu_table_json.biom -o DE_OTUs.txt -c not-real -x Control -y Fast  < /Users/caporaso/Dropbox/code/Qiime/qiime/support_files/R/fitZIG.r Program output:\r\n\r\nWarning messages:\r\n1: package ‘metagenomeSeq’ was built under R version 3.1.2\r\n2: package ‘BiocGenerics’ was built under R version 3.1.2\r\n3: package ‘RColorBrewer’ was built under R version 3.1.2\r\nError in `[.data.frame`(pData(MGS), , mapping_category) :\r\n undefined columns selected\r\nCalls: fitZIG -> which -> %in% -> match -> [ -> [.data.frame\r\nIn addition: Warning message:\r\nIn cumNormStat(MGS) : Low quantile estimate. Default value being used.\r\nExecution halted\r\n```\r\n\r\n- [x] when passing an invalid category value via `-x` or `-y`, the script doesn't error out and produces a statistics file with results that look somewhat valid\r\n\r\n- [x] it would help to break up the script description into paragraphs b/c it's currently hard to read\r\n\r\n@sowe9385 can you please work on this? We'll need this to be ready for the January 6th deadline @gregcaporaso mentioned in #1810.\r\n\r\n@gregcaporaso and I will continue adding to this list (we're still testing out this new script).\r\n\r\ncc @antgonza "},"comment":{"url":"https://api.github.com/repos/biocore/qiime/issues/comments/69220784","html_url":"https://github.com/biocore/qiime/issues/1813#issuecomment-69220784","issue_url":"https://api.github.com/repos/biocore/qiime/issues/1813","id":69220784,"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},"created_at":"2015-01-08T18:02:44Z","updated_at":"2015-01-08T18:02:44Z","body":"Fixed in #1820 "}}