{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbb/issues/95","labels_url":"https://api.github.com/repos/chapmanb/bcbb/issues/95/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbb/issues/95/comments","events_url":"https://api.github.com/repos/chapmanb/bcbb/issues/95/events","html_url":"https://github.com/chapmanb/bcbb/issues/95","id":54379374,"number":95,"title":"CDS entries in GFF3 file are not merged to a CompoundLocation","user":{"login":"mikdur","id":4670719,"avatar_url":"https://avatars.githubusercontent.com/u/4670719?v=3","gravatar_id":"","url":"https://api.github.com/users/mikdur","html_url":"https://github.com/mikdur","followers_url":"https://api.github.com/users/mikdur/followers","following_url":"https://api.github.com/users/mikdur/following{/other_user}","gists_url":"https://api.github.com/users/mikdur/gists{/gist_id}","starred_url":"https://api.github.com/users/mikdur/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikdur/subscriptions","organizations_url":"https://api.github.com/users/mikdur/orgs","repos_url":"https://api.github.com/users/mikdur/repos","events_url":"https://api.github.com/users/mikdur/events{/privacy}","received_events_url":"https://api.github.com/users/mikdur/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-01-14T21:31:09Z","updated_at":"2015-06-18T15:43:48Z","closed_at":null,"body":"Given a gene that looks something like this in GFF3 notion:\r\n\r\n```\r\n##gff-version 3\r\nscf_001 maker   gene    36837   38790   .       +       .       ID=BN869_G00000007;Name=BN869_G00000007;\r\nscf_001 maker   mRNA    36837   38790   .       +       .       ID=BN869_T00000007_1;Parent=BN869_G00000007;Name=BN869_T00000007_1;\r\nscf_001 maker   exon    36837   37491   .       +       .       ID=BN869_T00000007_1:exon:0;Parent=BN869_T00000007_1;\r\nscf_001 maker   exon    37547   38790   .       +       .       ID=BN869_T00000007_1:exon:1;Parent=BN869_T00000007_1;\r\nscf_001 maker   CDS     36837   37491   .       +       0       ID=BN869_T00000007_1:cds;Parent=BN869_T00000007_1;\r\nscf_001 maker   CDS     37547   38790   .       +       2       ID=BN869_T00000007_1:cds;Parent=BN869_T00000007_1;\r\n```\r\n\r\nThe GFF parser fails to join the two CDSs with the same ID into a single feature with a CompoundLocation. The result of this is that GenBank och EMBL files produced when merging (and flattening) GFF3 annotations get multiple CDSs where the CDS position instead should be a join, eg:\r\n\r\n```\r\nFT   CDS             join(36837..37491,37547..38790)\r\n```\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbb/issues/comments/113197198","html_url":"https://github.com/chapmanb/bcbb/issues/95#issuecomment-113197198","issue_url":"https://api.github.com/repos/chapmanb/bcbb/issues/95","id":113197198,"user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"created_at":"2015-06-18T15:43:48Z","updated_at":"2015-06-18T15:43:48Z","body":"@chapmanb yes I'm developing currently some Galaxy integration for gffutils, but this is lacking the conversion features as far as I know. You can not convert a gff-sqlite to genbank, isn't it?"}}