{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/37","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/37/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/37/events","html_url":"https://github.com/cjfields/redmine-test/issues/37","id":95098919,"number":37,"title":"multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Category:%20Bio::Search/Bio::SearchIO","name":"Category: Bio::Search/Bio::SearchIO","color":"00CC99"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Component:%20URL","name":"Component: URL","color":"ededed"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Normal","name":"Priority: Normal","color":"666600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Bug","name":"Tracker: Bug","color":"FF0000"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/cjfields/redmine-test/milestones/5","html_url":"https://github.com/cjfields/redmine-test/milestones/1.5%20branch","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/5/labels","id":1208470,"number":5,"title":"1.5 branch","description":null,"creator":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":0,"state":"open","created_at":"2015-07-15T03:42:39Z","updated_at":"2015-07-15T03:49:00Z","due_on":null,"closed_at":null},"comments":4,"created_at":"2015-07-15T03:49:00Z","updated_at":"2015-07-15T03:49:01Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Bernd empty** (Bernd empty)\nOriginal Redmine Issue: 2439, https://redmine.open-bio.org/issues/2439\nOriginal Date: 2008-02-01\nOriginal Assignee: Bioperl Guts\n\n---\n\nHi,\n\nAttached code and input with 2 BLAST results.\nI run this as: perl -w HTMLWriter.pl < blast2.txt > out.html\nI noticed the following issues with SearchIO and HTMLWriter:\n\n1) after the first BLAST result an end_report is called which should not be the case. Also the Search Parameters section is empty here:\nSearch Parameters\nParameter\tValue\n\nSearch Statistics\nStatistic\tValue\n\nBTW: this is also the case for a single FastA result.\n\n\n2) The Links to the alignments on the E-values are not report specific, but are the hit IDs. This is actually also the case on the NCBI BLAST server and causes the same problem on there: if an ID occurs in several reports the link sends us to the first occurrence, which in the attached example is always the first report.\n\n3) The (SearchIO) parsing of the hit ID and description could be improved for hits with concatenated descriptions. \nFor example, the following description from the original attached BLAST report is changed into a single long description line.\n\n>pdb|1JTM|A Chain A, Alternative Structures Of A Sequence Extended T4 Lysozyme \nShow That The Highly Conserved Beta-Sheet Has Weak Intrinsic \nFolding Propensity\n pdb|1JTN|A Chain A, Alternative Structures Of A Sequence Extended T4 Lysozyme \nShow That The Highly Conserved Beta-Sheet Region Has Weak \nIntrinsic Folding Propensity\n pdb|1JTN|B Chain B, Alternative Structures Of A Sequence Extended T4 Lysozyme \nShow That The Highly Conserved Beta-Sheet Region Has Weak \nIntrinsic Folding Propensity\n\nHowever, based on the indentation we can see what the new IDs and descriptions are. I'd propose storing this info by concatenating the other hits to the first description with <soh> as is done in the NCBI BLAST DB.\nThis way, SearchIO, will now contain the first ID as ID and the rest as description, where new hit IDs are seperated by <soh>. (This is an SearchIO issue). Now in HTMLWriter, we can  use these <soh> tags to print the hit description as in the original BLAST: each new ID indented and starting on a new line. This would make the HTML result from NR databases much more readable. We could print the IDs bold or link them. \n\n\nKind regards,\nBernd\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/121478473","html_url":"https://github.com/cjfields/redmine-test/issues/37#issuecomment-121478473","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/37","id":121478473,"user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"created_at":"2015-07-15T03:49:01Z","updated_at":"2015-07-15T03:49:01Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Jason Stajich** (@hyphaltip)\nOriginal Date: 2008-05-12T11:38:22Z\n\n---\n\nIt was never my intention to have > 1 report in an HTML file, but we can try and unroll part of that assumption looks like Chris has gotten that going."}}