{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/29301370","id":29301370,"diff_hunk":"@@ -557,6 +563,10 @@\n \n @register_sniffer('fasta')\n def _fasta_sniffer(fh):\n+\n+    if _count_blank_lines(fh) > 5:","path":"skbio/io/fasta.py","position":31,"original_position":31,"commit_id":"dffe07fee2db3105bcf2a381d941bad485c6cab9","original_commit_id":"dffe07fee2db3105bcf2a381d941bad485c6cab9","user":{"login":"anderspitman","id":7820200,"avatar_url":"https://avatars.githubusercontent.com/u/7820200?v=3","gravatar_id":"","url":"https://api.github.com/users/anderspitman","html_url":"https://github.com/anderspitman","followers_url":"https://api.github.com/users/anderspitman/followers","following_url":"https://api.github.com/users/anderspitman/following{/other_user}","gists_url":"https://api.github.com/users/anderspitman/gists{/gist_id}","starred_url":"https://api.github.com/users/anderspitman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anderspitman/subscriptions","organizations_url":"https://api.github.com/users/anderspitman/orgs","repos_url":"https://api.github.com/users/anderspitman/repos","events_url":"https://api.github.com/users/anderspitman/events{/privacy}","received_events_url":"https://api.github.com/users/anderspitman/received_events","type":"User","site_admin":false},"body":"@jairideout I don't think there's a simple way to move the `max_blank` logic up to `_line_generator`. The problem is that the sniffer doesn't use `_line_generator` directly, so there's no where to capture a return value and indicate the file was not identified by the sniffer. So the only way I thought to do it was have `_line_generator` raise an exception and have the sniffer catch it. But then the files always except, not just when being sniffed. I haven't been able to come up with a way to branch that logic.","created_at":"2015-04-29T00:10:42Z","updated_at":"2015-04-29T00:10:42Z","html_url":"https://github.com/biocore/scikit-bio/pull/893#discussion_r29301370","pull_request_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/893","_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/29301370"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/893#discussion_r29301370"},"pull_request":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/893"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/893","id":32733960,"html_url":"https://github.com/biocore/scikit-bio/pull/893","diff_url":"https://github.com/biocore/scikit-bio/pull/893.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/893.patch","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/893","number":893,"state":"open","locked":false,"title":"Allow newlines when reading fasta files","user":{"login":"anderspitman","id":7820200,"avatar_url":"https://avatars.githubusercontent.com/u/7820200?v=3","gravatar_id":"","url":"https://api.github.com/users/anderspitman","html_url":"https://github.com/anderspitman","followers_url":"https://api.github.com/users/anderspitman/followers","following_url":"https://api.github.com/users/anderspitman/following{/other_user}","gists_url":"https://api.github.com/users/anderspitman/gists{/gist_id}","starred_url":"https://api.github.com/users/anderspitman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anderspitman/subscriptions","organizations_url":"https://api.github.com/users/anderspitman/orgs","repos_url":"https://api.github.com/users/anderspitman/repos","events_url":"https://api.github.com/users/anderspitman/events{/privacy}","received_events_url":"https://api.github.com/users/anderspitman/received_events","type":"User","site_admin":false},"body":"For #781. Still need to do fastq and docs, but wanted to get preliminary feedback on the approach.\r\n\r\nMy algorithm was basically that newlines are fine unless they immediately precede a sequence line. That seems to match all the test cases @ebolyen specified, and I've added or modified the unit tests accordingly.","created_at":"2015-04-07T05:09:02Z","updated_at":"2015-04-29T00:10:42Z","closed_at":null,"merged_at":null,"merge_commit_sha":"05562eaf2508e2ad24ae0e709aae16952c4c850d","assignee":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/biocore/scikit-bio/milestones/13","html_url":"https://github.com/biocore/scikit-bio/milestones/0.3.0:%20Sequences,%20Collections,%20and%20Alignments,%20oh%20my!","labels_url":"https://api.github.com/repos/biocore/scikit-bio/milestones/13/labels","id":976974,"number":13,"title":"0.3.0: Sequences, Collections, and Alignments, oh my!","description":"Clean up `Alignment` API and better integrate alignment algorithms with sequence objects and collections.","creator":{"login":"ebolyen","id":3976804,"avatar_url":"https://avatars.githubusercontent.com/u/3976804?v=3","gravatar_id":"","url":"https://api.github.com/users/ebolyen","html_url":"https://github.com/ebolyen","followers_url":"https://api.github.com/users/ebolyen/followers","following_url":"https://api.github.com/users/ebolyen/following{/other_user}","gists_url":"https://api.github.com/users/ebolyen/gists{/gist_id}","starred_url":"https://api.github.com/users/ebolyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ebolyen/subscriptions","organizations_url":"https://api.github.com/users/ebolyen/orgs","repos_url":"https://api.github.com/users/ebolyen/repos","events_url":"https://api.github.com/users/ebolyen/events{/privacy}","received_events_url":"https://api.github.com/users/ebolyen/received_events","type":"User","site_admin":false},"open_issues":28,"closed_issues":28,"state":"open","created_at":"2015-02-12T15:40:43Z","updated_at":"2015-04-27T22:22:33Z","due_on":"2015-04-01T07:00:00Z","closed_at":null},"commits_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/893/commits","review_comments_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/893/comments","review_comment_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments{/number}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/893/comments","statuses_url":"https://api.github.com/repos/biocore/scikit-bio/statuses/dffe07fee2db3105bcf2a381d941bad485c6cab9","head":{"label":"anderspitman:fasta_ignore_blank_lines","ref":"fasta_ignore_blank_lines","sha":"dffe07fee2db3105bcf2a381d941bad485c6cab9","user":{"login":"anderspitman","id":7820200,"avatar_url":"https://avatars.githubusercontent.com/u/7820200?v=3","gravatar_id":"","url":"https://api.github.com/users/anderspitman","html_url":"https://github.com/anderspitman","followers_url":"https://api.github.com/users/anderspitman/followers","following_url":"https://api.github.com/users/anderspitman/following{/other_user}","gists_url":"https://api.github.com/users/anderspitman/gists{/gist_id}","starred_url":"https://api.github.com/users/anderspitman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anderspitman/subscriptions","organizations_url":"https://api.github.com/users/anderspitman/orgs","repos_url":"https://api.github.com/users/anderspitman/repos","events_url":"https://api.github.com/users/anderspitman/events{/privacy}","received_events_url":"https://api.github.com/users/anderspitman/received_events","type":"User","site_admin":false},"repo":{"id":28160892,"name":"scikit-bio","full_name":"anderspitman/scikit-bio","owner":{"login":"anderspitman","id":7820200,"avatar_url":"https://avatars.githubusercontent.com/u/7820200?v=3","gravatar_id":"","url":"https://api.github.com/users/anderspitman","html_url":"https://github.com/anderspitman","followers_url":"https://api.github.com/users/anderspitman/followers","following_url":"https://api.github.com/users/anderspitman/following{/other_user}","gists_url":"https://api.github.com/users/anderspitman/gists{/gist_id}","starred_url":"https://api.github.com/users/anderspitman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anderspitman/subscriptions","organizations_url":"https://api.github.com/users/anderspitman/orgs","repos_url":"https://api.github.com/users/anderspitman/repos","events_url":"https://api.github.com/users/anderspitman/events{/privacy}","received_events_url":"https://api.github.com/users/anderspitman/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/anderspitman/scikit-bio","description":"Core objects, functions and statistics for working with biological data in Python.","fork":true,"url":"https://api.github.com/repos/anderspitman/scikit-bio","forks_url":"https://api.github.com/repos/anderspitman/scikit-bio/forks","keys_url":"https://api.github.com/repos/anderspitman/scikit-bio/keys{/key_id}","collaborators_url":"https://api.github.com/repos/anderspitman/scikit-bio/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/anderspitman/scikit-bio/teams","hooks_url":"https://api.github.com/repos/anderspitman/scikit-bio/hooks","issue_events_url":"https://api.github.com/repos/anderspitman/scikit-bio/issues/events{/number}","events_url":"https://api.github.com/repos/anderspitman/scikit-bio/events","assignees_url":"https://api.github.com/repos/anderspitman/scikit-bio/assignees{/user}","branches_url":"https://api.github.com/repos/anderspitman/scikit-bio/branches{/branch}","tags_url":"https://api.github.com/repos/anderspitman/scikit-bio/tags","blobs_url":"https://api.github.com/repos/anderspitman/scikit-bio/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/anderspitman/scikit-bio/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/anderspitman/scikit-bio/git/refs{/sha}","trees_url":"https://api.github.com/repos/anderspitman/scikit-bio/git/trees{/sha}","statuses_url":"https://api.github.com/repos/anderspitman/scikit-bio/statuses/{sha}","languages_url":"https://api.github.com/repos/anderspitman/scikit-bio/languages","stargazers_url":"https://api.github.com/repos/anderspitman/scikit-bio/stargazers","contributors_url":"https://api.github.com/repos/anderspitman/scikit-bio/contributors","subscribers_url":"https://api.github.com/repos/anderspitman/scikit-bio/subscribers","subscription_url":"https://api.github.com/repos/anderspitman/scikit-bio/subscription","commits_url":"https://api.github.com/repos/anderspitman/scikit-bio/commits{/sha}","git_commits_url":"https://api.github.com/repos/anderspitman/scikit-bio/git/commits{/sha}","comments_url":"https://api.github.com/repos/anderspitman/scikit-bio/comments{/number}","issue_comment_url":"https://api.github.com/repos/anderspitman/scikit-bio/issues/comments{/number}","contents_url":"https://api.github.com/repos/anderspitman/scikit-bio/contents/{+path}","compare_url":"https://api.github.com/repos/anderspitman/scikit-bio/compare/{base}...{head}","merges_url":"https://api.github.com/repos/anderspitman/scikit-bio/merges","archive_url":"https://api.github.com/repos/anderspitman/scikit-bio/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/anderspitman/scikit-bio/downloads","issues_url":"https://api.github.com/repos/anderspitman/scikit-bio/issues{/number}","pulls_url":"https://api.github.com/repos/anderspitman/scikit-bio/pulls{/number}","milestones_url":"https://api.github.com/repos/anderspitman/scikit-bio/milestones{/number}","notifications_url":"https://api.github.com/repos/anderspitman/scikit-bio/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/anderspitman/scikit-bio/labels{/name}","releases_url":"https://api.github.com/repos/anderspitman/scikit-bio/releases{/id}","created_at":"2014-12-17T23:59:49Z","updated_at":"2015-03-13T00:43:46Z","pushed_at":"2015-04-26T05:22:00Z","git_url":"git://github.com/anderspitman/scikit-bio.git","ssh_url":"git@github.com:anderspitman/scikit-bio.git","clone_url":"https://github.com/anderspitman/scikit-bio.git","svn_url":"https://github.com/anderspitman/scikit-bio","homepage":"http://scikit-bio.org","size":33616,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"biocore:master","ref":"master","sha":"190e957ba6e7836d5e5ce2e702901b328ccbcc01","user":{"login":"biocore","id":6241857,"avatar_url":"https://avatars.githubusercontent.com/u/6241857?v=3","gravatar_id":"","url":"https://api.github.com/users/biocore","html_url":"https://github.com/biocore","followers_url":"https://api.github.com/users/biocore/followers","following_url":"https://api.github.com/users/biocore/following{/other_user}","gists_url":"https://api.github.com/users/biocore/gists{/gist_id}","starred_url":"https://api.github.com/users/biocore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocore/subscriptions","organizations_url":"https://api.github.com/users/biocore/orgs","repos_url":"https://api.github.com/users/biocore/repos","events_url":"https://api.github.com/users/biocore/events{/privacy}","received_events_url":"https://api.github.com/users/biocore/received_events","type":"Organization","site_admin":false},"repo":{"id":15168264,"name":"scikit-bio","full_name":"biocore/scikit-bio","owner":{"login":"biocore","id":6241857,"avatar_url":"https://avatars.githubusercontent.com/u/6241857?v=3","gravatar_id":"","url":"https://api.github.com/users/biocore","html_url":"https://github.com/biocore","followers_url":"https://api.github.com/users/biocore/followers","following_url":"https://api.github.com/users/biocore/following{/other_user}","gists_url":"https://api.github.com/users/biocore/gists{/gist_id}","starred_url":"https://api.github.com/users/biocore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocore/subscriptions","organizations_url":"https://api.github.com/users/biocore/orgs","repos_url":"https://api.github.com/users/biocore/repos","events_url":"https://api.github.com/users/biocore/events{/privacy}","received_events_url":"https://api.github.com/users/biocore/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/biocore/scikit-bio","description":"Core objects, functions and statistics for working with biological data in Python.","fork":false,"url":"https://api.github.com/repos/biocore/scikit-bio","forks_url":"https://api.github.com/repos/biocore/scikit-bio/forks","keys_url":"https://api.github.com/repos/biocore/scikit-bio/keys{/key_id}","collaborators_url":"https://api.github.com/repos/biocore/scikit-bio/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/biocore/scikit-bio/teams","hooks_url":"https://api.github.com/repos/biocore/scikit-bio/hooks","issue_events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/events{/number}","events_url":"https://api.github.com/repos/biocore/scikit-bio/events","assignees_url":"https://api.github.com/repos/biocore/scikit-bio/assignees{/user}","branches_url":"https://api.github.com/repos/biocore/scikit-bio/branches{/branch}","tags_url":"https://api.github.com/repos/biocore/scikit-bio/tags","blobs_url":"https://api.github.com/repos/biocore/scikit-bio/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/biocore/scikit-bio/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/biocore/scikit-bio/git/refs{/sha}","trees_url":"https://api.github.com/repos/biocore/scikit-bio/git/trees{/sha}","statuses_url":"https://api.github.com/repos/biocore/scikit-bio/statuses/{sha}","languages_url":"https://api.github.com/repos/biocore/scikit-bio/languages","stargazers_url":"https://api.github.com/repos/biocore/scikit-bio/stargazers","contributors_url":"https://api.github.com/repos/biocore/scikit-bio/contributors","subscribers_url":"https://api.github.com/repos/biocore/scikit-bio/subscribers","subscription_url":"https://api.github.com/repos/biocore/scikit-bio/subscription","commits_url":"https://api.github.com/repos/biocore/scikit-bio/commits{/sha}","git_commits_url":"https://api.github.com/repos/biocore/scikit-bio/git/commits{/sha}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/comments{/number}","issue_comment_url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments{/number}","contents_url":"https://api.github.com/repos/biocore/scikit-bio/contents/{+path}","compare_url":"https://api.github.com/repos/biocore/scikit-bio/compare/{base}...{head}","merges_url":"https://api.github.com/repos/biocore/scikit-bio/merges","archive_url":"https://api.github.com/repos/biocore/scikit-bio/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/biocore/scikit-bio/downloads","issues_url":"https://api.github.com/repos/biocore/scikit-bio/issues{/number}","pulls_url":"https://api.github.com/repos/biocore/scikit-bio/pulls{/number}","milestones_url":"https://api.github.com/repos/biocore/scikit-bio/milestones{/number}","notifications_url":"https://api.github.com/repos/biocore/scikit-bio/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/biocore/scikit-bio/labels{/name}","releases_url":"https://api.github.com/repos/biocore/scikit-bio/releases{/id}","created_at":"2013-12-13T16:24:41Z","updated_at":"2015-04-27T22:22:34Z","pushed_at":"2015-04-28T14:41:56Z","git_url":"git://github.com/biocore/scikit-bio.git","ssh_url":"git@github.com:biocore/scikit-bio.git","clone_url":"https://github.com/biocore/scikit-bio.git","svn_url":"https://github.com/biocore/scikit-bio","homepage":"http://scikit-bio.org","size":38336,"stargazers_count":122,"watchers_count":122,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":62,"mirror_url":null,"open_issues_count":128,"forks":62,"open_issues":128,"watchers":122,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/893"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/893"},"issue":{"href":"https://api.github.com/repos/biocore/scikit-bio/issues/893"},"comments":{"href":"https://api.github.com/repos/biocore/scikit-bio/issues/893/comments"},"review_comments":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/893/comments"},"review_comment":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/893/commits"},"statuses":{"href":"https://api.github.com/repos/biocore/scikit-bio/statuses/dffe07fee2db3105bcf2a381d941bad485c6cab9"}}}}