{"action":"opened","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/19","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/19/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/19/events","html_url":"https://github.com/cjfields/redmine-test/issues/19","id":95098351,"number":19,"title":"Bio::Seq object loses sequence data when blessed as Bio::Seq::Meta::Array","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/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/2","html_url":"https://github.com/cjfields/redmine-test/milestones/unspecified","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/2/labels","id":1208466,"number":2,"title":"unspecified","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":6,"closed_issues":0,"state":"open","created_at":"2015-07-15T03:32:05Z","updated_at":"2015-07-15T03:41:26Z","due_on":null,"closed_at":null},"comments":3,"created_at":"2015-07-15T03:41:26Z","updated_at":"2015-07-15T03:41:27Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Roy Chaudhuri** (Roy Chaudhuri)\nOriginal Redmine Issue: 2262, https://redmine.open-bio.org/issues/2262\nOriginal Date: 2007-04-04\nOriginal Assignee: Bioperl Guts\n\n---\n\nWhen I bless a Bio::Seq object as a Bio::Seq::Meta::Array (as instructed by the POD) it loses the primary sequence information (and other PrimarySeqI information such as length and accession). Features and annotation are not affected.\n\nBio::Seq::Meta suffers from a worse bug- Bio::SeqIO warns that the Bio::Seq::Meta object is not SeqI compliant. This seems to be due to the omission of Bio::Seq from the use base line in Bio::Seq::Meta (but not Bio::Seq::Meta::Array). When I add Bio::Seq into the use base line the behaviour is the same as for Bio::Seq::Meta::Array.\n\nThe following code demonstrates the problem:\n\n#!/usr/bin/perl\nuse warnings;\nuse strict;\nuse Bio::SeqIO;\nuse Bio::Seq::Meta::Array;\nmy $seq=Bio::SeqIO->new(-fh=>\\*ARGV, -format=>'genbank')->next_seq;\nbless $seq, 'Bio::Seq::Meta::Array';\nBio::SeqIO->new(-format=>'genbank')->write_seq($seq);\n\n\n"}}