{"action":"opened","issue":{"url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/issues/20","labels_url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/issues/20/comments","events_url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/issues/20/events","html_url":"https://github.com/HenrikBengtsson/aroma.seq/issues/20","id":74214054,"number":20,"title":"Is genome assembly important enough to become first class citizen?","user":{"login":"HenrikBengtsson","id":1616850,"avatar_url":"https://avatars.githubusercontent.com/u/1616850?v=3","gravatar_id":"","url":"https://api.github.com/users/HenrikBengtsson","html_url":"https://github.com/HenrikBengtsson","followers_url":"https://api.github.com/users/HenrikBengtsson/followers","following_url":"https://api.github.com/users/HenrikBengtsson/following{/other_user}","gists_url":"https://api.github.com/users/HenrikBengtsson/gists{/gist_id}","starred_url":"https://api.github.com/users/HenrikBengtsson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/HenrikBengtsson/subscriptions","organizations_url":"https://api.github.com/users/HenrikBengtsson/orgs","repos_url":"https://api.github.com/users/HenrikBengtsson/repos","events_url":"https://api.github.com/users/HenrikBengtsson/events{/privacy}","received_events_url":"https://api.github.com/users/HenrikBengtsson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/labels/help%20wanted","name":"help wanted","color":"159818"},{"url":"https://api.github.com/repos/HenrikBengtsson/aroma.seq/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-05-08T03:31:22Z","updated_at":"2015-05-08T03:31:22Z","closed_at":null,"body":"When it comes to annotation data, in addition to a formal _organism_ label, should the genome _assembly_ label becomes a first class citizen, e.g.\r\n```\r\nannotationData/organisms/Homo_sapiens/GRCh18/\r\nannotationData/organisms/Homo_sapiens/GRCh19/\r\nannotationData/organisms/Homo_sapiens/GRCh38/\r\nannotationData/organisms/Mus_musculus/GRCm37/\r\nannotationData/organisms/Mus_musculus/GRCm38/\r\n```\r\n?  Then one could lookup annotation data as:\r\n```r\r\nfa <- FastaReferenceFile(organism=\"Homo_sapiens\", assembly=\"GRCh38\")\r\n```\r\nNote that it should be allowed to have tags in assembly directory names, e.g.\r\n```\r\nannotationData/organisms/Homo_sapiens/GRCh38,hg19/\r\n```\r\nand still have the above lookup find it.  It's only the GRC label that needs to be unique.\r\n\r\nIt might be that one has multiple sub alternatives, e.g.\r\n```\r\nannotationData/organisms/Homo_sapiens/GRCh38,hg19/Ensembl/71/\r\nannotationData/organisms/Homo_sapiens/GRCh38,hg19/Ensembl/75/\r\n```\r\nThen the following request is ambigous (unless one defines some unique ordering and picks the \"most recent\" one:\r\n```r\r\ngtf <- GtfDataFile(organism=\"Homo_sapiens\", assembly=\"GRCh18\")\r\n# Or equivalently\r\ngtf <- GtfDataFile(organism=fa)\r\n```\r\nTo specify Ensembl release 71, then one could use:\r\n```r\r\ngtf <- GtfDataFile(organism=\"Homo_sapiens\", assembly=\"GRCh18\", sub=c(\"Ensembl\", \"75\"))\r\n# Or equivalently\r\ngtf <- GtfDataFile(organism=fa, sub=c(\"Ensembl\", \"75\"))\r\n```\r\n\r\n\r\n\r\n"}}