{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/44","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/44/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/44/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/44/events","html_url":"https://github.com/cjfields/redmine-test/issues/44","id":108469738,"number":44,"title":"bp_genbank2gff3.pl,  inconsistent strands for Trans-spliced gene.","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/1","html_url":"https://github.com/cjfields/redmine-test/milestones/main-trunk","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1/labels","id":1324961,"number":1,"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":19,"closed_issues":0,"state":"open","created_at":"2015-09-26T14:12:01Z","updated_at":"2015-09-26T14:23:15Z","due_on":null,"closed_at":null},"comments":1,"created_at":"2015-09-26T14:23:15Z","updated_at":"2015-09-26T14:23:18Z","closed_at":null,"body":"---\n\n\nAuthor Name: **liyankai empty** (liyankai empty)\nOriginal Redmine Issue: 3144, https://redmine.open-bio.org/issues/3144\nOriginal Date: 2010-10-07\nOriginal Assignee: Chris Mungall\n\n---\n\nDear Sir,\n\nwe are using bp\\_genbank2gff3.pl to load genbank file into chado. However, the script keeps giving an error message as shown below, it seems to us that the script can not handle “Trans-spliced gene”, which is gene rps12 in the genbank file (ftp://ftp.ncbi.nih.gov/genomes/Chloroplasts/plastids/plastids/\nNC\\_002762.gbk). Would you please tell us how we can get pass this.\n\nThank you very much for your prompt response.\n\nbest,\n\nyankai.\n\nNC\\_002762 Unflattening error:\nDetails:\n——————- EXCEPTION: Bio::Root::Exception ——————-\nMSG: PROBLEM, SEVERITY==1\ninconsistent strands. Trans-spliced gene? Range: [67272,67385] [125870,126092] [126633,126664]\nSTACK: Error::throw\nSTACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368\nSTACK: Bio::SeqFeature::Tools::Unflattener::problem /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:952\nSTACK: Bio::SeqFeature::Tools::Unflattener::\\_check\\_order\\_is\\_consistent /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2750\nSTACK: Bio::SeqFeature::Tools::Unflattener::infer\\_mRNA\\_from\\_CDS /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2641\nSTACK: Bio::SeqFeature::Tools::Unflattener::unflatten\\_seq /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:1529\nSTACK: main::unflatten\\_seq /usr/local/bin/bp\\_genbank2gff3.pl:915\nSTACK: /usr/local/bin/bp\\_genbank2gff3.pl:411\n—————————————————————————————-\n\n\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/143452490","html_url":"https://github.com/cjfields/redmine-test/issues/44#issuecomment-143452490","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/44","id":143452490,"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":"2015-09-26T14:23:18Z","updated_at":"2015-09-26T14:23:18Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Jason Stajich** (Jason Stajich)\nOriginal Date: 2011-03-11T20:27:08Z\n\n---\n\nPossible that Chris can take a look at the Unflattener code?\n\n"}}