{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/39","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/39/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/39/events","html_url":"https://github.com/cjfields/redmine-test/issues/39","id":95351351,"number":39,"title":"Enhancement to Bio::SeqIO::abi - abi_with_trace","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:%20bioperl-ext","name":"Category: bioperl-ext","color":"000099"},{"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:%20Migrate","name":"Tracker: Migrate","color":"ededed"}],"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":1210610,"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":11,"closed_issues":0,"state":"open","created_at":"2015-07-16T04:54:06Z","updated_at":"2015-07-16T05:06:33Z","due_on":null,"closed_at":null},"comments":9,"created_at":"2015-07-16T05:06:33Z","updated_at":"2015-07-16T05:06:55Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Chris Bailey** (Chris Bailey)\nOriginal Redmine Issue: 2329, https://redmine.open-bio.org/issues/2329\nOriginal Date: 2007-07-05\nOriginal Assignee: Bioperl Guts\n\n---\n\nI have created a seqIO module to enable the reading of trace data from abi files. This module makes use of the Staden io\\_lib as utilised in Bio::SeqIO::staden::read\n\nThe additional module requires updates to two modules, Bio::SeqIO::Staden::read.pm from bioperl-ext which now has extra inline c code to harvest the information from the staden io lib, along with a perl accessor function. Bio::Seq::Quality, which adds extra lines to -\\>new in order to read in trace\\_data if it’s provided, and a get\\_trace\\_graph function to return an array of values for each graph.\n\nthe new module is called abi\\_with\\_trace, and can be called in the usuall manner\nBio::SeqIO-\\>new( -file =\\> ‘file’, -format =\\> ‘abi\\_with\\_trace’);\n\n\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/121830864","html_url":"https://github.com/cjfields/redmine-test/issues/39#issuecomment-121830864","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/39","id":121830864,"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":"2015-07-16T05:06:55Z","updated_at":"2015-07-16T05:06:55Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Chris Fields** (Chris Fields)\nOriginal Date: 2007-07-05T09:05:36Z\n\n---\n\nOne thing to note: the io\\_lib version used in bioperl-ext is 1.8; newer io\\_lib versions (most recent is 1.10.1) aren’t compatible. bioperl-ext does work with some gentle prodding on Mac OS X using io\\_lib 1.8 but Inline might complain a bit.\n\nUpdating bioperl-ext to use more recent versions of io\\_lib is one of our outstanding issues, so feel free to check it out if you’re interested.\n\n"}}