{"action":"created","issue":{"url":"https://api.github.com/repos/bioperl/bioperl-live/issues/129","labels_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/129/labels{/name}","comments_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/129/comments","events_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/129/events","html_url":"https://github.com/bioperl/bioperl-live/issues/129","id":112643062,"number":129,"title":"Bio::SearchIO::hmmer3.pm writing unparsable lines to stdout","user":{"login":"JoeCarlson","id":3506317,"avatar_url":"https://avatars.githubusercontent.com/u/3506317?v=3","gravatar_id":"","url":"https://api.github.com/users/JoeCarlson","html_url":"https://github.com/JoeCarlson","followers_url":"https://api.github.com/users/JoeCarlson/followers","following_url":"https://api.github.com/users/JoeCarlson/following{/other_user}","gists_url":"https://api.github.com/users/JoeCarlson/gists{/gist_id}","starred_url":"https://api.github.com/users/JoeCarlson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JoeCarlson/subscriptions","organizations_url":"https://api.github.com/users/JoeCarlson/orgs","repos_url":"https://api.github.com/users/JoeCarlson/repos","events_url":"https://api.github.com/users/JoeCarlson/events{/privacy}","received_events_url":"https://api.github.com/users/JoeCarlson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-10-21T17:46:22Z","updated_at":"2015-11-03T12:59:05Z","closed_at":null,"body":"Hello,\r\n\r\nThanks for all the work.\r\n\r\nI've just run into a minor annoyance: When Bio::SearchIO::hmmer3.pm finds a line that it cannot parse, it writes that line to stdout along with the message 'Missed this line:' Lines 622 and 768 from the source code are examples.\r\n\r\nThis is messing up my downstream parsing. Can this to redirected to stderr or somehow treated better?\r\n\r\nThe particular lines that is causing problems are from hmmscan 3.1b1 which looks like:\r\n\r\n>> 2fo7A00\r\n[No individual domains that satisfy reporting thresholds (although complete target did)]\r\n\r\nI can deal with it in my local copy, but this seems like something that should be handled differently."},"comment":{"url":"https://api.github.com/repos/bioperl/bioperl-live/issues/comments/153344214","html_url":"https://github.com/bioperl/bioperl-live/issues/129#issuecomment-153344214","issue_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/129","id":153344214,"user":{"login":"pcantalupo","id":310962,"avatar_url":"https://avatars.githubusercontent.com/u/310962?v=3","gravatar_id":"","url":"https://api.github.com/users/pcantalupo","html_url":"https://github.com/pcantalupo","followers_url":"https://api.github.com/users/pcantalupo/followers","following_url":"https://api.github.com/users/pcantalupo/following{/other_user}","gists_url":"https://api.github.com/users/pcantalupo/gists{/gist_id}","starred_url":"https://api.github.com/users/pcantalupo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcantalupo/subscriptions","organizations_url":"https://api.github.com/users/pcantalupo/orgs","repos_url":"https://api.github.com/users/pcantalupo/repos","events_url":"https://api.github.com/users/pcantalupo/events{/privacy}","received_events_url":"https://api.github.com/users/pcantalupo/received_events","type":"User","site_admin":false},"created_at":"2015-11-03T12:59:05Z","updated_at":"2015-11-03T12:59:05Z","body":"@JoeCarlson can you create two gists for your input file and script? It is practically impossible to copy and paste them into an editor (especially the script). Thank you"}}