{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/235","labels_url":"https://api.github.com/repos/arq5x/bedtools2/issues/235/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/bedtools2/issues/235/comments","events_url":"https://api.github.com/repos/arq5x/bedtools2/issues/235/events","html_url":"https://github.com/arq5x/bedtools2/issues/235","id":75784047,"number":235,"title":"bedtools intersect fails when GFF file contains a ##FASTA section","user":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/arq5x/bedtools2/milestones/1","html_url":"https://github.com/arq5x/bedtools2/milestones/2.25.0","labels_url":"https://api.github.com/repos/arq5x/bedtools2/milestones/1/labels","id":1137888,"number":1,"title":"2.25.0","description":null,"creator":{"login":"arq5x","id":72291,"avatar_url":"https://avatars.githubusercontent.com/u/72291?v=3","gravatar_id":"","url":"https://api.github.com/users/arq5x","html_url":"https://github.com/arq5x","followers_url":"https://api.github.com/users/arq5x/followers","following_url":"https://api.github.com/users/arq5x/following{/other_user}","gists_url":"https://api.github.com/users/arq5x/gists{/gist_id}","starred_url":"https://api.github.com/users/arq5x/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arq5x/subscriptions","organizations_url":"https://api.github.com/users/arq5x/orgs","repos_url":"https://api.github.com/users/arq5x/repos","events_url":"https://api.github.com/users/arq5x/events{/privacy}","received_events_url":"https://api.github.com/users/arq5x/received_events","type":"User","site_admin":false},"open_issues":7,"closed_issues":1,"state":"open","created_at":"2015-05-28T12:21:12Z","updated_at":"2015-06-04T09:57:49Z","due_on":null,"closed_at":null},"comments":11,"created_at":"2015-05-13T00:00:08Z","updated_at":"2015-06-14T01:49:56Z","closed_at":null,"body":"```\r\n❯❯❯ bedtools intersect -v -a a.gff -b b.gff\r\nError: line number 11752 of file a.gff has 1 fields, but 9 were expected.\r\n```\r\n\r\n### a.gff\r\n```\r\n…\r\n38\tprokka\tgene\t981\t1121\t.\t-\t1\tID=OU3MT_05875_gene;locus_tag=OU3MT_05875\r\n##FASTA\r\n>1\r\nTTACAAGCTTGAAAGAATGAATGACATCCTTTTTCTTCCCTCAATGCTATAGAAATAAGG\r\n…\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/comments/111769581","html_url":"https://github.com/arq5x/bedtools2/issues/235#issuecomment-111769581","issue_url":"https://api.github.com/repos/arq5x/bedtools2/issues/235","id":111769581,"user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"created_at":"2015-06-14T01:49:56Z","updated_at":"2015-06-14T01:49:56Z","body":"It's not 100% clear from the GFF3 spec if you can **not** have the ```FASTA``` section and still put ```>fasta``` sequences at the end anyway.  I've seen files like that. And BioPerl allows it when parsing in.\r\n\r\nYou've probably never seen it because it doesn't make sense for massive genomes with long term references. But for bacteria, the genomes are equally frequent as the annotations!\r\n "}}