{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/893","repository_url":"https://api.github.com/repos/biopython/biopython","labels_url":"https://api.github.com/repos/biopython/biopython/issues/893/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/893/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/893/events","html_url":"https://github.com/biopython/biopython/issues/893","id":167217812,"number":893,"title":"Blast NCBIXML parser sets HSP gaps varyingly as int or tuple","user":{"login":"twrightsman","id":6300973,"avatar_url":"https://avatars.githubusercontent.com/u/6300973?v=3","gravatar_id":"","url":"https://api.github.com/users/twrightsman","html_url":"https://github.com/twrightsman","followers_url":"https://api.github.com/users/twrightsman/followers","following_url":"https://api.github.com/users/twrightsman/following{/other_user}","gists_url":"https://api.github.com/users/twrightsman/gists{/gist_id}","starred_url":"https://api.github.com/users/twrightsman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/twrightsman/subscriptions","organizations_url":"https://api.github.com/users/twrightsman/orgs","repos_url":"https://api.github.com/users/twrightsman/repos","events_url":"https://api.github.com/users/twrightsman/events{/privacy}","received_events_url":"https://api.github.com/users/twrightsman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-07-24T05:20:20Z","updated_at":"2016-07-24T05:26:55Z","closed_at":null,"body":"Migrated from https://redmine.open-bio.org/issues/3363\r\n\r\n@etal said:\r\n> As described in Bio.Blast.Record, the (obsolete) plain-text Blast parser sets the hsp.gaps attribute as a tuple of (gaps, total aligned), while the NCBIXML parser sets the same attribute as the integer number of gaps when the Hsp_gaps element is parsed. However, the Blast XML report omits this element if there are no gaps in a hit, and so the value of hsps.gaps remains the surprising default value (None, None) instead of an integer.\r\n> \r\n> To avoid breaking the plain-text parser, I would guess the best approach is to set the value of hsp.gaps to 0 initially in the NCBIXML parser."},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/234758603","html_url":"https://github.com/biopython/biopython/issues/893#issuecomment-234758603","issue_url":"https://api.github.com/repos/biopython/biopython/issues/893","id":234758603,"user":{"login":"twrightsman","id":6300973,"avatar_url":"https://avatars.githubusercontent.com/u/6300973?v=3","gravatar_id":"","url":"https://api.github.com/users/twrightsman","html_url":"https://github.com/twrightsman","followers_url":"https://api.github.com/users/twrightsman/followers","following_url":"https://api.github.com/users/twrightsman/following{/other_user}","gists_url":"https://api.github.com/users/twrightsman/gists{/gist_id}","starred_url":"https://api.github.com/users/twrightsman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/twrightsman/subscriptions","organizations_url":"https://api.github.com/users/twrightsman/orgs","repos_url":"https://api.github.com/users/twrightsman/repos","events_url":"https://api.github.com/users/twrightsman/events{/privacy}","received_events_url":"https://api.github.com/users/twrightsman/received_events","type":"User","site_admin":false},"created_at":"2016-07-24T05:26:55Z","updated_at":"2016-07-24T05:26:55Z","body":"@etal replied:\r\n\r\n> Wibowo Arindrarto wrote:\r\n> \r\n>> Thanks Eric! I added the test into test_NCBIXML with your test case here: https://github.com/bow/biopython/commit/69659e8569987829330d0c455d8abce64c1fdd30\r\n> \r\n> Thanks, looks good to me. I guess we can close this bug when your branch is merged, then?"}}
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