{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/86893763","pull_request_review_id":7528848,"id":86893763,"diff_hunk":"@@ -39,47 +37,113 @@\n --------------------\n **State: Experimental as of 0.4.1.**\n \n-The International Nucleotide Sequence Database Collaboration (INSDC)\n-foundational initiative between the DDBJ, EMBL, and GenBank\n-(http://www.insdc.org/). These organisations all use the\n-same \"Feature Table\" layout in their plain text flat file formats.\n-\n-However, the header and sequence sections of an EMBL file are very\n-different in layout to those produced by GenBank/DDBJ.\n-\n-Feature Table Documentation:\n-http://www.insdc.org/files/feature_table.html\n-ftp://ftp.ncbi.nih.gov/genbank/docs/FTv10_3.html\n-\n-The sequence in the ``'ORIGIN'`` section is always in lowercase for the\n-GenBank files downloaded from NCBI. For the RNA molecules, ``'t'`` (thymine),\n-instead of ``'u'`` (uracil) is used in the sequence. All GenBank writers\n-follow these conventions while writing GenBank files.\n-\n-All the sections before ``'FEATURES'`` will be read into ``metadata`` of\n-``Sequence`` or its sub-class. The header and its content of a section\n-is stored as a pair of key and value in ``metadata``. For the ``'REFERENCE'``\n+Sections before ``FEATURES``\n+^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n+All the sections before ``FEATURES`` will be read into the attribute\n+of ``metadata``. The header and its content of a section is stored as\n+a pair of key and value in ``metadata``. For the ``REFERENCE``\n section, its value is stored as a list, as there are often multiple\n reference sections in one GenBank record.\n \n-The information of the ``'FEATURES'`` is stored in both ``metadata`` and\n-``positional_metadata`` of ``Sequence`` or its sub-class. For each feature,\n-its location is stored as boolean column in ``positional_metadata``; other\n-qualifiers are stored as a ``dict`` in the ``list`` of\n-``metadata['FEATURES']``. In the ``dict`` of qualifiers, there are a few\n-extra keys, which end with ``'_'``, including:\n+``FEATURES`` section\n+^^^^^^^^^^^^^^^^^^^^\n+The International Nucleotide Sequence Database Collaboration (INSDC\n+[2]_) foundational initiative between the DDBJ, EMBL, and","path":"skbio/io/format/genbank.py","position":69,"original_position":69,"commit_id":"e0c1cd7593eeea04b4daed3532ac4a8be8062c18","original_commit_id":"e0c1cd7593eeea04b4daed3532ac4a8be8062c18","user":{"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},"body":"Sentence fragment.","created_at":"2016-11-07T23:29:35Z","updated_at":"2016-11-07T23:51:52Z","html_url":"https://github.com/biocore/scikit-bio/pull/1440#discussion_r86893763","pull_request_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440","_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/86893763"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/1440#discussion_r86893763"},"pull_request":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440","id":89920140,"html_url":"https://github.com/biocore/scikit-bio/pull/1440","diff_url":"https://github.com/biocore/scikit-bio/pull/1440.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/1440.patch","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1440","number":1440,"state":"open","locked":false,"title":"update genbank parser to use `IntervalMetadata`","user":{"login":"RNAer","id":1000056,"avatar_url":"https://avatars.githubusercontent.com/u/1000056?v=3","gravatar_id":"","url":"https://api.github.com/users/RNAer","html_url":"https://github.com/RNAer","followers_url":"https://api.github.com/users/RNAer/followers","following_url":"https://api.github.com/users/RNAer/following{/other_user}","gists_url":"https://api.github.com/users/RNAer/gists{/gist_id}","starred_url":"https://api.github.com/users/RNAer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RNAer/subscriptions","organizations_url":"https://api.github.com/users/RNAer/orgs","repos_url":"https://api.github.com/users/RNAer/repos","events_url":"https://api.github.com/users/RNAer/events{/privacy}","received_events_url":"https://api.github.com/users/RNAer/received_events","type":"User","site_admin":false},"body":"also cleans up the code a bit.\n","created_at":"2016-10-18T23:57:07Z","updated_at":"2016-11-07T23:51:52Z","closed_at":null,"merged_at":null,"merge_commit_sha":"10478637bd75b8e8d6eee85592e6923de66c3dd8","assignee":{"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},"assignees":[{"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}],"milestone":null,"commits_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440/commits","review_comments_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440/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/1440/comments","statuses_url":"https://api.github.com/repos/biocore/scikit-bio/statuses/e0c1cd7593eeea04b4daed3532ac4a8be8062c18","head":{"label":"RNAer:mixin","ref":"mixin","sha":"e0c1cd7593eeea04b4daed3532ac4a8be8062c18","user":{"login":"RNAer","id":1000056,"avatar_url":"https://avatars.githubusercontent.com/u/1000056?v=3","gravatar_id":"","url":"https://api.github.com/users/RNAer","html_url":"https://github.com/RNAer","followers_url":"https://api.github.com/users/RNAer/followers","following_url":"https://api.github.com/users/RNAer/following{/other_user}","gists_url":"https://api.github.com/users/RNAer/gists{/gist_id}","starred_url":"https://api.github.com/users/RNAer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RNAer/subscriptions","organizations_url":"https://api.github.com/users/RNAer/orgs","repos_url":"https://api.github.com/users/RNAer/repos","events_url":"https://api.github.com/users/RNAer/events{/privacy}","received_events_url":"https://api.github.com/users/RNAer/received_events","type":"User","site_admin":false},"repo":{"id":20581004,"name":"scikit-bio","full_name":"RNAer/scikit-bio","owner":{"login":"RNAer","id":1000056,"avatar_url":"https://avatars.githubusercontent.com/u/1000056?v=3","gravatar_id":"","url":"https://api.github.com/users/RNAer","html_url":"https://github.com/RNAer","followers_url":"https://api.github.com/users/RNAer/followers","following_url":"https://api.github.com/users/RNAer/following{/other_user}","gists_url":"https://api.github.com/users/RNAer/gists{/gist_id}","starred_url":"https://api.github.com/users/RNAer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RNAer/subscriptions","organizations_url":"https://api.github.com/users/RNAer/orgs","repos_url":"https://api.github.com/users/RNAer/repos","events_url":"https://api.github.com/users/RNAer/events{/privacy}","received_events_url":"https://api.github.com/users/RNAer/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/RNAer/scikit-bio","description":"Core objects, functions and statistics for working with biological data in Python.","fork":true,"url":"https://api.github.com/repos/RNAer/scikit-bio","forks_url":"https://api.github.com/repos/RNAer/scikit-bio/forks","keys_url":"https://api.github.com/repos/RNAer/scikit-bio/keys{/key_id}","collaborators_url":"https://api.github.com/repos/RNAer/scikit-bio/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/RNAer/scikit-bio/teams","hooks_url":"https://api.github.com/repos/RNAer/scikit-bio/hooks","issue_events_url":"https://api.github.com/repos/RNAer/scikit-bio/issues/events{/number}","events_url":"https://api.github.com/repos/RNAer/scikit-bio/events","assignees_url":"https://api.github.com/repos/RNAer/scikit-bio/assignees{/user}","branches_url":"https://api.github.com/repos/RNAer/scikit-bio/branches{/branch}","tags_url":"https://api.github.com/repos/RNAer/scikit-bio/tags","blobs_url":"https://api.github.com/repos/RNAer/scikit-bio/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/RNAer/scikit-bio/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/RNAer/scikit-bio/git/refs{/sha}","trees_url":"https://api.github.com/repos/RNAer/scikit-bio/git/trees{/sha}","statuses_url":"https://api.github.com/repos/RNAer/scikit-bio/statuses/{sha}","languages_url":"https://api.github.com/repos/RNAer/scikit-bio/languages","stargazers_url":"https://api.github.com/repos/RNAer/scikit-bio/stargazers","contributors_url":"https://api.github.com/repos/RNAer/scikit-bio/contributors","subscribers_url":"https://api.github.com/repos/RNAer/scikit-bio/subscribers","subscription_url":"https://api.github.com/repos/RNAer/scikit-bio/subscription","commits_url":"https://api.github.com/repos/RNAer/scikit-bio/commits{/sha}","git_commits_url":"https://api.github.com/repos/RNAer/scikit-bio/git/commits{/sha}","comments_url":"https://api.github.com/repos/RNAer/scikit-bio/comments{/number}","issue_comment_url":"https://api.github.com/repos/RNAer/scikit-bio/issues/comments{/number}","contents_url":"https://api.github.com/repos/RNAer/scikit-bio/contents/{+path}","compare_url":"https://api.github.com/repos/RNAer/scikit-bio/compare/{base}...{head}","merges_url":"https://api.github.com/repos/RNAer/scikit-bio/merges","archive_url":"https://api.github.com/repos/RNAer/scikit-bio/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/RNAer/scikit-bio/downloads","issues_url":"https://api.github.com/repos/RNAer/scikit-bio/issues{/number}","pulls_url":"https://api.github.com/repos/RNAer/scikit-bio/pulls{/number}","milestones_url":"https://api.github.com/repos/RNAer/scikit-bio/milestones{/number}","notifications_url":"https://api.github.com/repos/RNAer/scikit-bio/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/RNAer/scikit-bio/labels{/name}","releases_url":"https://api.github.com/repos/RNAer/scikit-bio/releases{/id}","deployments_url":"https://api.github.com/repos/RNAer/scikit-bio/deployments","created_at":"2014-06-06T23:24:15Z","updated_at":"2016-10-31T16:35:12Z","pushed_at":"2016-10-31T16:35:09Z","git_url":"git://github.com/RNAer/scikit-bio.git","ssh_url":"git@github.com:RNAer/scikit-bio.git","clone_url":"https://github.com/RNAer/scikit-bio.git","svn_url":"https://github.com/RNAer/scikit-bio","homepage":"http://scikit-bio.org","size":24395,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"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":"3125f3fbfe6495c5f532ecaee5a50f8f638363bd","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":"scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.","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}","deployments_url":"https://api.github.com/repos/biocore/scikit-bio/deployments","created_at":"2013-12-13T16:24:41Z","updated_at":"2016-11-06T07:59:22Z","pushed_at":"2016-10-28T17:13:16Z","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":43372,"stargazers_count":241,"watchers_count":241,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":110,"mirror_url":null,"open_issues_count":166,"forks":110,"open_issues":166,"watchers":241,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/1440"},"issue":{"href":"https://api.github.com/repos/biocore/scikit-bio/issues/1440"},"comments":{"href":"https://api.github.com/repos/biocore/scikit-bio/issues/1440/comments"},"review_comments":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/1440/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/1440/commits"},"statuses":{"href":"https://api.github.com/repos/biocore/scikit-bio/statuses/e0c1cd7593eeea04b4daed3532ac4a8be8062c18"}}}}
{"actor":{"display_login":"ebolyen"}}