{"action":"created","issue":{"url":"https://api.github.com/repos/daler/gffutils/issues/42","labels_url":"https://api.github.com/repos/daler/gffutils/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/daler/gffutils/issues/42/comments","events_url":"https://api.github.com/repos/daler/gffutils/issues/42/events","html_url":"https://github.com/daler/gffutils/issues/42","id":53910498,"number":42,"title":"Inserting/shifting annotations","user":{"login":"rmzelle","id":77951,"avatar_url":"https://avatars.githubusercontent.com/u/77951?v=3","gravatar_id":"","url":"https://api.github.com/users/rmzelle","html_url":"https://github.com/rmzelle","followers_url":"https://api.github.com/users/rmzelle/followers","following_url":"https://api.github.com/users/rmzelle/following{/other_user}","gists_url":"https://api.github.com/users/rmzelle/gists{/gist_id}","starred_url":"https://api.github.com/users/rmzelle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmzelle/subscriptions","organizations_url":"https://api.github.com/users/rmzelle/orgs","repos_url":"https://api.github.com/users/rmzelle/repos","events_url":"https://api.github.com/users/rmzelle/events{/privacy}","received_events_url":"https://api.github.com/users/rmzelle/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/daler/gffutils/labels/feature%20request","name":"feature request","color":"444444"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":19,"created_at":"2015-01-09T20:21:45Z","updated_at":"2015-01-26T17:35:06Z","closed_at":null,"body":"In my field of research, it is very common to remove and/or insert custom DNA sequences in microbial genomes. I would like to make the same changes *in silico* in the FASTA file of the reference genome, as well as in the accompanying GFF annotation file.\r\n\r\nTo make this easy, I would love the following features:\r\n\r\n* conversion of GenBank annotations to the GFF format, since we save our genomic modifications in GenBank format. For this I found http://biopython.org/wiki/GFF_Parsing#Converting_other_formats_to_GFF3 (the author mentions at https://github.com/chapmanb/bcbb/tree/master/gff that he hopes to eventually integrate this code into gffutils).\r\n* an easy way to introduce annotations from a second GFF file (describing the newly introduced sequence) at a specified location in the first GFF file (describing the genome). For example, I might want to replace a 4 kb gene in GFF file A by a 14 kb DNA fragment described in GFF file B. It would be great if gffutils had functions for: a) deleting annotations that fall in the deleted 4 kb region, b) deleting, splitting, or stretching annotations that partially overlap or span the deleted 4 kb region, c) shifting the coordinates of any annotations downstream of the 4 kb integration site by 10 kb (14 - 4 kb), and d) adding the annotations from GFF file B to GFF file A while updating their coordinates.\r\n\r\nDoes this fall in the scope of gffutils, or are my requests too esoteric? I guess the simplest feature request would be the ability to easily select and/or shift annotations that start beyond a certain coordinate. (I realize that I can already make such changes by iterating over each feature, but it would still be nice to have such a function)"},"comment":{"url":"https://api.github.com/repos/daler/gffutils/issues/comments/71501252","html_url":"https://github.com/daler/gffutils/issues/42#issuecomment-71501252","issue_url":"https://api.github.com/repos/daler/gffutils/issues/42","id":71501252,"user":{"login":"rmzelle","id":77951,"avatar_url":"https://avatars.githubusercontent.com/u/77951?v=3","gravatar_id":"","url":"https://api.github.com/users/rmzelle","html_url":"https://github.com/rmzelle","followers_url":"https://api.github.com/users/rmzelle/followers","following_url":"https://api.github.com/users/rmzelle/following{/other_user}","gists_url":"https://api.github.com/users/rmzelle/gists{/gist_id}","starred_url":"https://api.github.com/users/rmzelle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmzelle/subscriptions","organizations_url":"https://api.github.com/users/rmzelle/orgs","repos_url":"https://api.github.com/users/rmzelle/repos","events_url":"https://api.github.com/users/rmzelle/events{/privacy}","received_events_url":"https://api.github.com/users/rmzelle/received_events","type":"User","site_admin":false},"created_at":"2015-01-26T17:35:06Z","updated_at":"2015-01-26T17:35:06Z","body":"I'll let you know if I notice anything off."}}