{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/588","labels_url":"https://api.github.com/repos/biopython/biopython/issues/588/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/588/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/588/events","html_url":"https://github.com/biopython/biopython/issues/588","id":98399457,"number":588,"title":"SearchIO hmmer3-text fails when phmmer runs with '-A' option","user":{"login":"JoaoRodrigues","id":237328,"avatar_url":"https://avatars.githubusercontent.com/u/237328?v=3","gravatar_id":"","url":"https://api.github.com/users/JoaoRodrigues","html_url":"https://github.com/JoaoRodrigues","followers_url":"https://api.github.com/users/JoaoRodrigues/followers","following_url":"https://api.github.com/users/JoaoRodrigues/following{/other_user}","gists_url":"https://api.github.com/users/JoaoRodrigues/gists{/gist_id}","starred_url":"https://api.github.com/users/JoaoRodrigues/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JoaoRodrigues/subscriptions","organizations_url":"https://api.github.com/users/JoaoRodrigues/orgs","repos_url":"https://api.github.com/users/JoaoRodrigues/repos","events_url":"https://api.github.com/users/JoaoRodrigues/events{/privacy}","received_events_url":"https://api.github.com/users/JoaoRodrigues/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-07-31T14:11:39Z","updated_at":"2015-08-01T10:25:25Z","closed_at":null,"body":"Maybe this has been reported before or it is in the pipeline but a quick search here in the issues list didn't show much. This bug is reproduced with the lasted git version.\r\n\r\nIf phmmer runs with the `-A` option, it adds a comment right before the last line of the output file that breaks the SearchIO HMMER3 text parser.\r\n\r\n```\r\n# CPU time: 1.21u 1.30s 00:00:02.51 Elapsed: 00:00:02.54\r\n# Mc/sec: 3430.94\r\n//\r\n# Alignment of 168 hits satisfying inclusion thresholds saved to: psa.sto\r\n[ok]\r\n```\r\n\r\nThe parser complains during the `_parse_qresult` method, when trying to find the `qid` attribute. Basically, it does not expect a comment line after '//'. I guess the parser is built this way to handle jackhmmer output. Adding a simple '#'-ignore statement afterwards would fix this, but there might a more elegant solution (@peterjc @bow) :)\r\n"},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/126895392","html_url":"https://github.com/biopython/biopython/issues/588#issuecomment-126895392","issue_url":"https://api.github.com/repos/biopython/biopython/issues/588","id":126895392,"user":{"login":"JoaoRodrigues","id":237328,"avatar_url":"https://avatars.githubusercontent.com/u/237328?v=3","gravatar_id":"","url":"https://api.github.com/users/JoaoRodrigues","html_url":"https://github.com/JoaoRodrigues","followers_url":"https://api.github.com/users/JoaoRodrigues/followers","following_url":"https://api.github.com/users/JoaoRodrigues/following{/other_user}","gists_url":"https://api.github.com/users/JoaoRodrigues/gists{/gist_id}","starred_url":"https://api.github.com/users/JoaoRodrigues/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JoaoRodrigues/subscriptions","organizations_url":"https://api.github.com/users/JoaoRodrigues/orgs","repos_url":"https://api.github.com/users/JoaoRodrigues/repos","events_url":"https://api.github.com/users/JoaoRodrigues/events{/privacy}","received_events_url":"https://api.github.com/users/JoaoRodrigues/received_events","type":"User","site_admin":false},"created_at":"2015-08-01T10:25:25Z","updated_at":"2015-08-01T10:25:25Z","body":"I can share mine, quite small. \n\n\nCheers and thanks!\n\nOn Sat, Aug 1, 2015 at 11:50 AM, Wibowo Arindrarto\n<notifications@github.com> wrote:\n\n> Hey @JoaoRodrigues,\n> Yes, I can confirm this on HMMER 3.1b2. We did not have test cases for any `phmmer` output, it turns out. I'll generate some test cases and make a fix this over the weekend.\n> ---\n> Reply to this email directly or view it on GitHub:\n> https://github.com/biopython/biopython/issues/588#issuecomment-126892814"}}