{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/10","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/10/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/10/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/10/events","html_url":"https://github.com/cjfields/redmine-test/issues/10","id":108254209,"number":10,"title":"Bio::ClusterIO::dbsnp breaks with new XML output","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:%20Core%20Components","name":"Category: Core Components","color":"006699"},{"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/2","html_url":"https://github.com/cjfields/redmine-test/milestones/main-trunk","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/2/labels","id":1323219,"number":2,"title":"main-trunk","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":2,"closed_issues":0,"state":"open","created_at":"2015-09-25T03:16:25Z","updated_at":"2015-09-25T03:17:37Z","due_on":null,"closed_at":null},"comments":14,"created_at":"2015-09-25T03:17:37Z","updated_at":"2015-09-25T03:18:12Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Chris Fields** (Chris Fields)\nOriginal Redmine Issue: 2018, https://redmine.open-bio.org/issues/2018\nOriginal Date: 2006-06-07\nOriginal Assignee: Bioperl Guts\n\n---\n\nThe dbSNP XML schema at NCBI has changed recently (Oct. 2005) (no longer uses DTD). Bio::ClusterIO::dbsnp breaks with new XML output from NCBI.\n\nUsing the old LittleChrY.dbsnp.xml (in t\\\\data in bioperl-live), everything works. next\\_cluster returns a Bio::Variation::SNP object\n\nUsing the attached file (new XML) as input and using Data::Dumper as shown below, get undef returned (probably should throw something instead here).\n\ntest script\n——————————————-\n\\#! perl\nuse strict;\nuse warnings;\nuse Bio::ClusterIO;\nuse Data::Dumper;\nmy $cl\\_in = Bio::ClusterIO-\\>new(-file =\\> shift,\n -format =\\> ‘dbsnp’);\n\nmy $cl\\_out = Bio::ClusterIO-\\>new(-fh =\\> \\\\\\*STDOUT,\n -format =\\> ‘unigene’);\nmy $cluster = $cl\\_in-\\>next\\_cluster;\nprint Dumper($cl\\_in);\nprint Dumper($cluster);\n——————————————-\n\n\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/143111167","html_url":"https://github.com/cjfields/redmine-test/issues/10#issuecomment-143111167","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/10","id":143111167,"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":"2015-09-25T03:18:12Z","updated_at":"2015-09-25T03:18:12Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Mark Johnson** (Mark Johnson)\nOriginal Date: 2007-03-19T18:06:57Z\n\n---\n\nHmmm. Maybe a bit of XSLT to go between the two formats and a new format option for Bio::ClusterIO would do the trick? The downside would be adding a dependency on an XSLT engine…I used libxslt from the Gnome project via XML::LibXSLT back in the day. Writing the XSLT would be the hard part…my XSLT kung-fu never was much good, and it’s **very** rusty now…if NCBI has such a critter, maybe they’d cough it up?\n\n"}}